☰ Navigation Tabs
Crystal structure of the metallo-beta-lactamase VIM1 with 2551
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 35.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.38 α = 90 b = 67.74 β = 93.56 c = 40.27 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 2019-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 1.32 40.19 98.9 0.06 0.066 0.026 0.999 14.8 6.4 48915 13.86
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 1.32 1.35 98 0.607 0.658 0.252 0.856 3.1 6.7
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 1.32 40.19 1.34 48880 2498 98.69 0.1434 0.1421 0.1427 0.1679 0.143 18.84
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 18.2268 f_angle_d 0.9843 f_chiral_restr 0.0793 f_plane_restr 0.0301 f_bond_d 0.0069
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1731 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 37
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing