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Crystal structure of NDM-9 metallo-beta-lactamase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 292 0.2M NaCl, 0.1M Phosphate/citrate pH 4.2, 20% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.19 43.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.929 α = 90 b = 122.929 β = 90 c = 38.501 γ = 120
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-F 2017-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.72931 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.43 61.46 99.8 0.083 0.088 0.99 16.5 9.2 120161 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.52 98.8 0.738 0.782 0.71 2.6 9.1
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 FREE R-VALUE 3q6x 1.43 61.46 117209 3004 99.82 0.07461 0.07351 0.0792 0.11632 0.1188 RANDOM 20.072
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] -3.26 -3.26 6.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.647 r_dihedral_angle_4_deg 20.607 r_rigid_bond_restr 18.943 r_dihedral_angle_3_deg 12.557 r_scbond_it 11.336 r_scbond_other 11.334 r_scangle_other 8.173 r_long_range_B_refined 7.906 r_long_range_B_other 7.905 r_dihedral_angle_1_deg 7.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.647 r_dihedral_angle_4_deg 20.607 r_rigid_bond_restr 18.943 r_dihedral_angle_3_deg 12.557 r_scbond_it 11.336 r_scbond_other 11.334 r_scangle_other 8.173 r_long_range_B_refined 7.906 r_long_range_B_other 7.905 r_dihedral_angle_1_deg 7.086 r_mcbond_it 5.766 r_mcbond_other 5.753 r_mcangle_it 5.36 r_mcangle_other 5.36 r_angle_refined_deg 1.758 r_angle_other_deg 1.586 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5081 Nucleic Acid Atoms Solvent Atoms 778 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing