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Crystal structure of the metallo-beta-lactamase VIM1 with 3062
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 1.91 35.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.42 α = 90 b = 67.83 β = 93.28 c = 40.08 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 2019-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 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 1.27 34.04 97.4 0.05 0.055 0.021 0.999 16.2 6.8 54022 14.74
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 1.27 1.3 89.5 0.869 0.959 0.395 0.708 1.8 5.6
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 1.27 28.9 1.35 54005 2674 97.41 0.1295 0.1282 0.1283 0.1558 0.1558 19.38
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 12.957 f_angle_d 1.5028 f_chiral_restr 0.1086 f_plane_restr 0.0137 f_bond_d 0.0132
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1731 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 33
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing