HEADER PROTEIN FIBRIL 29-MAY-21 7N2I TITLE MICROED STRUCTURE OF HUMAN LECT2 (45-53) PHASED BY ARCIMBOLDO-BORGES COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECT2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 45-53; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS MICROED, AMYLOID, LECT2, PROTEIN FIBRIL EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR L.S.RICHARDS,M.D.FLORES,C.T.ZEE,C.GLYNN,M.GALLAGHER-JONES,M.R.SAWAYA REVDAT 3 22-MAY-24 7N2I 1 REMARK REVDAT 2 10-MAY-23 7N2I 1 JRNL REVDAT 1 01-JUN-22 7N2I 0 JRNL AUTH L.S.RICHARDS,M.D.FLORES,C.MILLAN,C.GLYNN,C.T.ZEE,M.R.SAWAYA, JRNL AUTH 2 M.GALLAGHER-JONES,R.J.BORGES,I.USON,J.A.RODRIGUEZ JRNL TITL FRAGMENT-BASED AB INITIO PHASING OF PEPTIDIC NANOCRYSTALS BY JRNL TITL 2 MICROED. JRNL REF ACS BIO MED CHEM AU V. 3 201 2023 JRNL REFN ESSN 2694-2437 JRNL PMID 37096030 JRNL DOI 10.1021/ACSBIOMEDCHEMAU.2C00082 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 81.2 REMARK 3 NUMBER OF REFLECTIONS : 985 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.040 REMARK 3 FREE R VALUE TEST SET COUNT : 89 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 7.7540 - 2.9695 0.77 103 11 0.1354 0.1280 REMARK 3 2 2.9695 - 2.3794 0.77 75 7 0.1834 0.1803 REMARK 3 3 2.3794 - 2.0853 0.80 101 10 0.1996 0.1673 REMARK 3 4 2.0853 - 1.8977 0.81 94 9 0.2001 0.2017 REMARK 3 5 1.8977 - 1.7634 0.80 81 8 0.2457 0.1272 REMARK 3 6 1.7634 - 1.6605 0.84 79 8 0.2201 0.3715 REMARK 3 7 1.6605 - 1.5781 0.78 72 7 0.2465 0.2548 REMARK 3 8 1.5781 - 1.5099 0.88 99 10 0.2217 0.2996 REMARK 3 9 1.5099 - 1.4522 0.84 95 10 0.2414 0.1986 REMARK 3 10 1.4522 - 1.4024 0.85 97 9 0.2652 0.4549 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7N2I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000254609. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : FEI TALOS ARCTICA REMARK 240 DETECTOR TYPE : TVIPS TEMCAM-F416 (4K X 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : 986 REMARK 240 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 240 RESOLUTION RANGE LOW (A) : 7.754 REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 240 DATA REDUNDANCY : 4.218 REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :1.40 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :1.48 REMARK 240 COMPLETENESS FOR SHELL (%) : 82.8 REMARK 240 DATA REDUNDANCY IN SHELL : 4.17 REMARK 240 R MERGE FOR SHELL (I) : 0.38500 REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 240 SOFTWARE USED : NULL REMARK 240 STARTING MODEL : NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.20000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 2.36500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.20000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 2.36500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 5 56.62 -145.68 REMARK 500 REMARK 500 REMARK: NULL DBREF 7N2I A 0 8 PDB 7N2I 7N2I 0 8 SEQRES 1 A 9 GLY SER THR VAL TYR ALA PRO PHE THR FORMUL 2 HOH *2(H2 O) CRYST1 58.400 4.730 19.630 90.00 105.01 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017123 0.000000 0.004590 0.00000 SCALE2 0.000000 0.211416 0.000000 0.00000 SCALE3 0.000000 0.000000 0.052741 0.00000 ATOM 1 N GLY A 0 26.606 3.420 4.944 1.00 17.40 N ATOM 2 CA GLY A 0 25.680 3.579 6.048 1.00 13.53 C ATOM 3 C GLY A 0 24.611 2.507 6.061 1.00 9.49 C ATOM 4 O GLY A 0 24.436 1.777 5.091 1.00 14.50 O ATOM 5 N SER A 1 23.900 2.405 7.174 1.00 9.09 N ATOM 6 CA SER A 1 22.770 1.498 7.263 1.00 6.71 C ATOM 7 C SER A 1 21.495 2.223 6.868 1.00 5.68 C ATOM 8 O SER A 1 21.431 3.446 6.835 1.00 6.97 O ATOM 9 CB SER A 1 22.640 0.931 8.674 1.00 10.35 C ATOM 10 OG SER A 1 23.807 0.214 9.030 1.00 10.87 O ATOM 11 N THR A 2 20.472 1.448 6.570 1.00 6.39 N ATOM 12 CA THR A 2 19.253 1.994 6.017 1.00 5.89 C ATOM 13 C THR A 2 18.078 1.290 6.661 1.00 6.11 C ATOM 14 O THR A 2 18.082 0.067 6.803 1.00 6.07 O ATOM 15 CB THR A 2 19.199 1.731 4.506 1.00 8.91 C ATOM 16 OG1 THR A 2 20.373 2.268 3.884 1.00 10.62 O ATOM 17 CG2 THR A 2 17.968 2.356 3.890 1.00 9.10 C ATOM 18 N VAL A 3 17.080 2.066 7.061 1.00 6.44 N ATOM 19 CA VAL A 3 15.739 1.552 7.271 1.00 4.92 C ATOM 20 C VAL A 3 14.894 2.140 6.162 1.00 4.88 C ATOM 21 O VAL A 3 14.752 3.364 6.067 1.00 5.53 O ATOM 22 CB VAL A 3 15.186 1.912 8.653 1.00 5.32 C ATOM 23 CG1 VAL A 3 13.693 1.598 8.719 1.00 6.64 C ATOM 24 CG2 VAL A 3 15.948 1.149 9.725 1.00 5.37 C ATOM 25 N TYR A 4 14.396 1.285 5.294 1.00 5.33 N ATOM 26 CA TYR A 4 13.564 1.697 4.181 1.00 4.07 C ATOM 27 C TYR A 4 12.164 1.251 4.547 1.00 4.54 C ATOM 28 O TYR A 4 11.860 0.055 4.500 1.00 4.61 O ATOM 29 CB TYR A 4 14.026 1.006 2.907 1.00 6.66 C ATOM 30 CG TYR A 4 13.195 1.352 1.701 1.00 5.78 C ATOM 31 CD1 TYR A 4 13.546 2.405 0.876 1.00 7.04 C ATOM 32 CD2 TYR A 4 12.060 0.628 1.384 1.00 6.40 C ATOM 33 CE1 TYR A 4 12.799 2.713 -0.230 1.00 6.27 C ATOM 34 CE2 TYR A 4 11.299 0.939 0.278 1.00 8.08 C ATOM 35 CZ TYR A 4 11.668 1.988 -0.519 1.00 9.14 C ATOM 36 OH TYR A 4 10.909 2.298 -1.621 1.00 9.33 O ATOM 37 N ALA A 5 11.329 2.195 4.931 1.00 5.25 N ATOM 38 CA ALA A 5 10.005 1.805 5.369 1.00 4.19 C ATOM 39 C ALA A 5 8.974 2.852 4.979 1.00 3.96 C ATOM 40 O ALA A 5 8.249 3.349 5.847 1.00 5.30 O ATOM 41 CB ALA A 5 10.004 1.594 6.879 1.00 4.55 C ATOM 42 N PRO A 6 8.854 3.191 3.696 1.00 6.32 N ATOM 43 CA PRO A 6 7.727 4.027 3.279 1.00 4.06 C ATOM 44 C PRO A 6 6.441 3.306 3.620 1.00 4.35 C ATOM 45 O PRO A 6 6.356 2.082 3.547 1.00 4.89 O ATOM 46 CB PRO A 6 7.909 4.131 1.765 1.00 6.70 C ATOM 47 CG PRO A 6 8.585 2.862 1.402 1.00 5.20 C ATOM 48 CD PRO A 6 9.543 2.609 2.534 1.00 5.92 C ATOM 49 N PHE A 7 5.431 4.064 4.009 1.00 6.10 N ATOM 50 CA PHE A 7 4.224 3.384 4.421 1.00 6.14 C ATOM 51 C PHE A 7 2.996 4.209 4.106 1.00 8.04 C ATOM 52 O PHE A 7 3.073 5.409 3.841 1.00 7.03 O ATOM 53 CB PHE A 7 4.272 2.963 5.888 1.00 7.89 C ATOM 54 CG PHE A 7 4.344 4.099 6.874 1.00 8.64 C ATOM 55 CD1 PHE A 7 3.188 4.616 7.439 1.00 9.74 C ATOM 56 CD2 PHE A 7 5.567 4.593 7.296 1.00 8.41 C ATOM 57 CE1 PHE A 7 3.249 5.631 8.373 1.00 8.14 C ATOM 58 CE2 PHE A 7 5.633 5.614 8.230 1.00 7.87 C ATOM 59 CZ PHE A 7 4.475 6.124 8.775 1.00 8.52 C ATOM 60 N THR A 8 1.860 3.522 4.105 1.00 10.75 N ATOM 61 CA THR A 8 0.557 4.153 4.058 1.00 16.25 C ATOM 62 C THR A 8 -0.311 3.374 5.031 1.00 20.10 C ATOM 63 O THR A 8 0.118 2.338 5.543 1.00 18.08 O ATOM 64 CB THR A 8 -0.084 4.082 2.657 1.00 22.95 C ATOM 65 OG1 THR A 8 -0.391 2.720 2.339 1.00 24.81 O ATOM 66 CG2 THR A 8 0.848 4.652 1.596 1.00 24.19 C ATOM 67 OXT THR A 8 -1.441 3.752 5.332 1.00 21.92 O TER 68 THR A 8 HETATM 69 O HOH A 101 20.665 3.540 1.987 1.00 13.76 O HETATM 70 O HOH A 102 4.629 1.501 1.407 1.00 11.55 O MASTER 191 0 0 0 0 0 0 6 69 1 0 1 END