☰ Navigation Tabs
Crystal structure of NDM-1 complexed with compound 5
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, HANGING DROP 293 0.1 M Bis Tris pH 7.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.604 α = 90 b = 58.486 β = 92.47 c = 61.761 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 2022-03-30 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 1.68 50 97.2 0.077 20.35 3.1 45520
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 1.68 1.71 0.368 2.38
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 1.68 42.48 43277 2227 96.49 0.229 0.22801 0.2352 0.24684 0.253 RANDOM 21.849
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] 0.31 0.5 -0.78 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.873 r_dihedral_angle_4_deg 18.837 r_dihedral_angle_3_deg 13.005 r_dihedral_angle_1_deg 6.385 r_long_range_B_refined 4.724 r_long_range_B_other 4.696 r_scangle_other 3.9 r_scbond_it 2.67 r_scbond_other 2.67 r_mcangle_other 2.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.873 r_dihedral_angle_4_deg 18.837 r_dihedral_angle_3_deg 13.005 r_dihedral_angle_1_deg 6.385 r_long_range_B_refined 4.724 r_long_range_B_other 4.696 r_scangle_other 3.9 r_scbond_it 2.67 r_scbond_other 2.67 r_mcangle_other 2.002 r_mcangle_it 2 r_angle_refined_deg 1.661 r_mcbond_it 1.53 r_mcbond_other 1.524 r_angle_other_deg 1.488 r_chiral_restr 0.08 r_bond_refined_d 0.029 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 337 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing