☰ Navigation Tabs
Crystal structure of the metallo-beta-lactamase VIM1 with 3027
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 1.93 36.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.51 α = 90 b = 68.06 β = 93.83 c = 40.31 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 2019-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979499 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 1.2 34.63 95.3 0.055 0.06 0.023 0.998 15.3 6.3 63365 13.63
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 1.2 1.22 64.1 0.6 0.72 0.388 0.645 1.8 3.1
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 1.2 34.63 1.1 61814 6121 94.14 0.1308 0.1302 0.1284 0.1428 0.1268 18.48
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 18.5127 f_angle_d 1.3459 f_chiral_restr 0.0958 f_plane_restr 0.0131 f_bond_d 0.0109
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1717 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing