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Crystal structure of IMP-1 metallo-beta-lactamase in a complex with MCR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Y5B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M sodium acetate, 0.1M sodium HEPES buffer (pH 7.5), 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.05 40.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.92 α = 90 b = 56.82 β = 90 c = 101.06 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 2M 2018-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A
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 1.57 56.82 100 0.064 22.2 11.3 29943
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 1.57 1.65 100 0.354 6.4 11.2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5Y5B 1.57 50.53 28368 1514 99.98 0.16654 0.16477 0.1781 0.19969 0.2108 RANDOM 22.085
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] -0.21 0.85 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.371 r_dihedral_angle_3_deg 14.386 r_dihedral_angle_4_deg 8.798 r_dihedral_angle_1_deg 7.749 r_long_range_B_refined 6.578 r_long_range_B_other 6.505 r_scangle_other 5.215 r_scbond_it 3.569 r_scbond_other 3.568 r_mcangle_it 3.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.371 r_dihedral_angle_3_deg 14.386 r_dihedral_angle_4_deg 8.798 r_dihedral_angle_1_deg 7.749 r_long_range_B_refined 6.578 r_long_range_B_other 6.505 r_scangle_other 5.215 r_scbond_it 3.569 r_scbond_other 3.568 r_mcangle_it 3.405 r_mcangle_other 3.405 r_mcbond_it 2.421 r_mcbond_other 2.41 r_angle_refined_deg 1.266 r_angle_other_deg 0.941 r_chiral_restr 0.279 r_gen_planes_refined 0.014 r_bond_refined_d 0.008 r_gen_planes_other 0.002 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1728 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing