☰ Navigation Tabs
Crystal structure of NDM-1 beta-lactamase in complex with broad spectrum boronic inhibitor cpd3
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
Crystal Properties Matthews coefficient Solvent content 1.96 37.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.425 α = 90 b = 73.95 β = 90 c = 77.687 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 2018-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97 ESRF ID29
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 53.56 97.24 0.059 0.999 14.12 5.7 212200 7.44
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 1.036 77.39 0.377 0.717 2.15 2.6
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 53.62 201126 11074 97.21 0.16643 0.16593 0.1681 0.17572 0.169 RANDOM 10.13
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] -0.05 -0.05 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.589 r_dihedral_angle_4_deg 19.97 r_dihedral_angle_3_deg 13.564 r_dihedral_angle_1_deg 6.459 r_long_range_B_refined 3.949 r_scbond_it 2.132 r_angle_refined_deg 1.987 r_mcangle_it 1.895 r_mcbond_it 1.259 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.589 r_dihedral_angle_4_deg 19.97 r_dihedral_angle_3_deg 13.564 r_dihedral_angle_1_deg 6.459 r_long_range_B_refined 3.949 r_scbond_it 2.132 r_angle_refined_deg 1.987 r_mcangle_it 1.895 r_mcbond_it 1.259 r_chiral_restr 0.114 r_bond_refined_d 0.015 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3420 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing