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Crystal Structure Of NDM-1 Metallo-beta-lactamase In Complex With Inhibitor X2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EYB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Ammonium Sulfate, 0.1M Bis-Tris [pH 6.1], 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.72 α = 90 b = 74.04 β = 90 c = 77.43 γ = 90
Symmetry Space Group P 21 21 21
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 1.76 77.43 100 0.12 14.8 10.3 40824
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 1.76 1.86 99.9 0.474 9.5
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 4eyb 1.763 53.513 40758 2034 99.971 0.15 0.148 0.1615 0.1916 0.2013 20.359
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] 0.145 -0.392 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.304 r_dihedral_angle_4_deg 19.688 r_dihedral_angle_3_deg 14.762 r_dihedral_angle_1_deg 8.088 r_lrange_it 5.691 r_lrange_other 5.638 r_scangle_it 3.991 r_scangle_other 3.991 r_scbond_it 2.732 r_scbond_other 2.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.304 r_dihedral_angle_4_deg 19.688 r_dihedral_angle_3_deg 14.762 r_dihedral_angle_1_deg 8.088 r_lrange_it 5.691 r_lrange_other 5.638 r_scangle_it 3.991 r_scangle_other 3.991 r_scbond_it 2.732 r_scbond_other 2.732 r_mcangle_other 2.696 r_mcangle_it 2.692 r_mcbond_it 1.896 r_mcbond_other 1.89 r_angle_refined_deg 1.365 r_angle_other_deg 1.334 r_nbd_other 0.237 r_symmetry_nbd_refined 0.235 r_nbd_refined 0.207 r_symmetry_nbd_other 0.201 r_symmetry_xyhbond_nbd_refined 0.197 r_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.158 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.081 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3537 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing