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Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins
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 5.8 295 28% (w/v) PEG3350, 0.1 M Bis-Tris, pH 5.8 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.9 35.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.62 α = 90 b = 77.57 β = 90 c = 132.31 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 IMAGE PLATE RIGAKU RAXIS IV++ 2012-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.008 38.785 99.43 26996 26843
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.008 2.12 92.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3Q6X 2.008 38.785 1.38 26996 26772 1345 97.68 0.1486 0.1486 0.1462 0.1486 0.1926 0.1946 random
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 14.294 f_angle_d 1.111 f_chiral_restr 0.046 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3594 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 54
Software Software Software Name Purpose CrystalClear data collection PHASES phasing PHENIX refinement MOSFLM data reduction SCALA data scaling