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Crystal structure of the metallo-beta-lactamase VIM-1 with 2492
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Experimentally determined structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 2.6M ammonium phosphate, 0.1M tris, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.422 α = 90 b = 67.859 β = 93.28 c = 40.149 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2025-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.78380 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.15 34.51 100 0.088 0.095 0.036 0.999 10.3 6.9 74815 10.37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.17 100 0.836 0.909 0.352 0.745 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.15 33.93 1.35 74782 7692 99.98 0.1286 0.1271 0.1328 0.1554 0.1532 15.47
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.2689 f_angle_d 1.1617 f_chiral_restr 0.0917 f_plane_restr 0.0119 f_bond_d 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1725 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PHENIX refinement pointless data scaling xia2 data reduction PHASER phasing PDB_EXTRACT data extraction