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Crystal structure of the metallo-beta-lactamase VIM1 with 3380
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 35.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.47 α = 90 b = 67.95 β = 93.78 c = 40.26 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 2020-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97965 Diamond I04
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 1.24 39.38 98.4 0.031 0.033 0.013 1 24.6 6.5 59078 12.91
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 1.24 1.27 82.6 0.287 0.325 0.148 0.922 4.1 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.24 29.1 1.35 59046 2966 98.43 0.1232 0.1223 0.1237 0.1418 0.1432 17.49
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 11.5965 f_angle_d 1.3437 f_chiral_restr 0.1078 f_plane_restr 0.0281 f_bond_d 0.0125
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1731 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing