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NDM-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements for the Hydrolysis of Penicillin versus Carbapenem Antibiotics
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, HANGING DROP 7 295 0.2 M LiCl, 0.1 M HEPES, pH7.0, 20% (w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 2.15 42.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.167 α = 92.23 b = 68.861 β = 77.026 c = 68.441 γ = 91.84
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2017-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1 ALS 8.2.1
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 1.75 48.668 91.07 0.053 17.6 2.3 75377 16.0102224723
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 1.75 1.813 54.76 0.325 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3Q6X 1.75006148726 37.2364552136 1.96361990839 75370 3746 91.0727663791 0.158241721583 0.156087511804 0.1564 0.19952021866 0.1992 19.4899005082
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.9981202544 f_angle_d 0.767076571585 f_chiral_restr 0.0531110621711 f_bond_d 0.00546008292878 f_plane_restr 0.00467596668114
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6818 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 26
Software Software Software Name Purpose phenix.refine refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing