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Crystal structure of NDM-1 complexed with compound 22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D19
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 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.772 α = 90 b = 58.685 β = 90.89 c = 62.242 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 PILATUS 6M 2022-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.978 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 1.78 50 98.1 0.067 21.63 4 38500
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 1.78 1.81 0.307 2.57
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 1.78 42.73 36491 1995 97.95 0.16373 0.16118 0.1692 0.21227 0.2182 RANDOM 24.912
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] -0.16 0.53 -1.8 1.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.331 r_dihedral_angle_4_deg 18.965 r_dihedral_angle_3_deg 14.061 r_dihedral_angle_1_deg 7.008 r_long_range_B_refined 5.033 r_long_range_B_other 4.977 r_scangle_other 4.082 r_scbond_it 2.813 r_scbond_other 2.802 r_mcangle_other 2.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.331 r_dihedral_angle_4_deg 18.965 r_dihedral_angle_3_deg 14.061 r_dihedral_angle_1_deg 7.008 r_long_range_B_refined 5.033 r_long_range_B_other 4.977 r_scangle_other 4.082 r_scbond_it 2.813 r_scbond_other 2.802 r_mcangle_other 2.527 r_mcangle_it 2.523 r_mcbond_it 1.847 r_mcbond_other 1.839 r_angle_refined_deg 1.622 r_angle_other_deg 1.44 r_chiral_restr 0.079 r_bond_refined_d 0.01 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 3404 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing