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Crystal structure of NDM-1 in complex with triazole-based inhibitor OP31
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.3 M MgCl2 exahydrate; 0.3 M CaCl2 dihydrate; 25% w/v PEG 3350; 25% w/v MPD; 20% v/v PEG 1000; 0.1 M MES/IMIDAZOLE pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.95 36.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.678 α = 90 b = 73.665 β = 90 c = 77.501 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-F 2019-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.001 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.33 42.42 97.4 0.04 0.999 10.3 1.9 89075
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.33 1.38 93.8 0.251 0.714 2.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6IBV 1.33 42.42 84461 4611 97.12 0.1865 0.1853 0.2073 0.1992 RANDOM 19.037
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] -0.86 -0.25 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.749 r_dihedral_angle_4_deg 17.652 r_dihedral_angle_3_deg 14.478 r_rigid_bond_restr 7.614 r_dihedral_angle_1_deg 6.641 r_angle_refined_deg 1.789 r_chiral_restr 0.11 r_gen_planes_refined 0.013 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3418 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHENIX phasing