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Crystal structure of the metallo-beta-lactamase VIM1 with 2652
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 2.2M ammonium phosphate 0.1M TrisHCl, pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.92 35.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.477 α = 90 b = 67.903 β = 93.58 c = 40.284 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 EIGER2 XE 16M 2019-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976246 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 1.25 29.06 96.6 0.033 0.035 0.014 0.999 37.2 6.5 56834 11.04
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 1.25 1.27 67 0.093 0.105 0.048 0.99 12.5 4.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.25 29.06 1.32 55701 5576 96 0.112 0.111 0.1317 0.1213 17.01
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 15.8708 f_angle_d 1.4394 f_chiral_restr 0.1087 f_plane_restr 0.0165 f_bond_d 0.0147
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1731 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing