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Crystal structure of the metallo-beta-lactamase VIM-2 with ML302F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BZ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1mM TCEP, 10mM ML302, 50mM HEPES pH 7.5, 100mM NaCl, 0.1mM ZnCl2, 0.1M magnesium formate, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.48 α = 90 b = 78.91 β = 130.48 c = 67.46 γ = 90
Symmetry Space Group C 1 2 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 2M 2014-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 2.14 51.32 98.2 0.112 0.154 0.106 0.982 8.7 3.4 22190
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 2.14 2.2 98.4 0.517 0.707 0.479 0.699 2.1 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4BZ3 2.14 51.312 1.34 22188 1107 98.02 0.1711 0.1691 0.1769 0.2096 0.2088 26.9173
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 11.098 f_angle_d 0.541 f_chiral_restr 0.046 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3482 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling REFMAC phasing