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Crystal structure of NDM-1 beta-lactamase in complex with boronic inhibitor cpd 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 293 0.3 M MgCl2 exahydrate; 0.3 M CaCl2 dihydrate; 25% w/v PEG 3350; 25% w/v MPD; 20% v/v PEG 1000; 0.1 M MES/IMIDAZOLE pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.25 α = 90 b = 73.748 β = 90 c = 77.276 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 6M 2018-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.00 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 42.52 98 0.039 0.999 20.3 4.5 64514 11.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.554 97.48 0.426 0.836 3.48 4.5
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 (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 5GZU 1.5 42.52 60635 3044 98.07 0.14159 0.13903 0.1443 0.19144 0.1942 RANDOM 18.388
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] 0.23 -0.69 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.905 r_dihedral_angle_4_deg 18.126 r_dihedral_angle_3_deg 15.302 r_rigid_bond_restr 11.521 r_dihedral_angle_1_deg 6.752 r_long_range_B_refined 4.92 r_scbond_it 3.832 r_mcangle_it 2.988 r_mcbond_it 2.461 r_angle_refined_deg 1.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.905 r_dihedral_angle_4_deg 18.126 r_dihedral_angle_3_deg 15.302 r_rigid_bond_restr 11.521 r_dihedral_angle_1_deg 6.752 r_long_range_B_refined 4.92 r_scbond_it 3.832 r_mcangle_it 2.988 r_mcbond_it 2.461 r_angle_refined_deg 1.945 r_chiral_restr 0.123 r_bond_refined_d 0.014 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3388 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing