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Crystal structure of NDM-12 metallo-beta-lactamase in complex with hydrolyzed ampicillin
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 7.5 292 0.15M KBr, 30% PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 1.87 34.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.469 α = 90 b = 76.449 β = 90 c = 130.906 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 PILATUS 2M 2017-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918400 BESSY 14.2
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 2.1 66.02 97.6 0.149 0.169 0.99 7 4.3 22766 -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 2.1 2.23 96.6 0.8 0.92 0.62 3.9
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 2.1 21.65 21606 1160 97.58 0.17499 0.17214 0.1786 0.22726 0.2308 RANDOM 33.59
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] -1.57 0.44 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.176 r_dihedral_angle_4_deg 17.608 r_dihedral_angle_3_deg 14.026 r_dihedral_angle_1_deg 7.393 r_long_range_B_refined 6.573 r_long_range_B_other 6.571 r_scangle_other 4.867 r_scbond_it 3.555 r_scbond_other 3.554 r_mcangle_other 3.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.176 r_dihedral_angle_4_deg 17.608 r_dihedral_angle_3_deg 14.026 r_dihedral_angle_1_deg 7.393 r_long_range_B_refined 6.573 r_long_range_B_other 6.571 r_scangle_other 4.867 r_scbond_it 3.555 r_scbond_other 3.554 r_mcangle_other 3.341 r_mcangle_it 3.34 r_mcbond_it 2.403 r_mcbond_other 2.401 r_angle_refined_deg 1.614 r_angle_other_deg 1.398 r_chiral_restr 0.067 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 3566 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing