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Crystal structure of NDM-1 complexed with compound 13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M Bis Tris pH 7.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.313 α = 90 b = 58.361 β = 93.4 c = 43.159 γ = 90
Symmetry Space Group P 1 21 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 6M 2022-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
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 1.84 50 97.4 0.104 14.19 3.5 17427
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 1.84 1.87 0.381 2.05
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.84 43.08 16591 821 97.19 0.1654 0.1627 0.1702 0.22203 0.2262 RANDOM 26.466
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] 1.19 0.64 -0.52 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.225 r_dihedral_angle_4_deg 17.123 r_dihedral_angle_3_deg 15.304 r_dihedral_angle_1_deg 6.734 r_long_range_B_other 5.022 r_long_range_B_refined 5.008 r_scangle_other 3.905 r_scbond_other 2.662 r_scbond_it 2.657 r_mcangle_other 2.521
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.225 r_dihedral_angle_4_deg 17.123 r_dihedral_angle_3_deg 15.304 r_dihedral_angle_1_deg 6.734 r_long_range_B_other 5.022 r_long_range_B_refined 5.008 r_scangle_other 3.905 r_scbond_other 2.662 r_scbond_it 2.657 r_mcangle_other 2.521 r_mcangle_it 2.516 r_mcbond_it 1.809 r_mcbond_other 1.799 r_angle_refined_deg 1.601 r_angle_other_deg 1.401 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1702 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing