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Crystal Structure Of VIM-2 Metallo-beta-lactamase In Complex With Inhibitor X2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M magnesium formate dihydrate, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.04 39.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.96 α = 90 b = 79.15 β = 138.4 c = 77.74 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 PILATUS3 S 6M 2017-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 55.46 99.6 0.079 13.7 5.2 65271
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 100 0.16 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4nq2 1.5 39.606 65267 3385 99.591 0.157 0.1552 0.1552 0.1829 0.1836 12.08
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] 0.325 0.007 -0.621 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.557 r_dihedral_angle_4_deg 22.378 r_dihedral_angle_3_deg 13.331 r_dihedral_angle_1_deg 7.602 r_lrange_it 4.709 r_lrange_other 4.709 r_scangle_it 3.222 r_scangle_other 3.222 r_dihedral_angle_other_3_deg 2.297 r_scbond_it 2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.557 r_dihedral_angle_4_deg 22.378 r_dihedral_angle_3_deg 13.331 r_dihedral_angle_1_deg 7.602 r_lrange_it 4.709 r_lrange_other 4.709 r_scangle_it 3.222 r_scangle_other 3.222 r_dihedral_angle_other_3_deg 2.297 r_scbond_it 2.18 r_scbond_other 2.18 r_mcangle_other 2.099 r_mcangle_it 2.098 r_angle_refined_deg 1.45 r_angle_other_deg 1.425 r_mcbond_other 1.364 r_mcbond_it 1.361 r_nbd_other 0.225 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_refined 0.204 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.154 r_symmetry_nbd_refined 0.095 r_metal_ion_refined 0.088 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3494 Nucleic Acid Atoms Solvent Atoms 567 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing