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Crystal Structure of New Delhi Metallo-beta-Lactamase-1 D223A mutant from Klebsiella pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q6X PDB entry 3Q6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2 M magnesium chloride, 0.1 M Bis-Tris pH 6.5, 25 %(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.91 35.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.14 α = 90 b = 74.225 β = 90.11 c = 76.599 γ = 90
Symmetry Space Group P 1 21 1
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 mirrors 2011-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.35 50 96.5 0.061 9.3 7.2 162811 162811 14.23
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.36 69.1 0.582 2 4 5774
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MIR THROUGHOUT PDB entry 3Q6X 1.351 34.036 162771 162771 8178 96.21 0.145 0.145 0.143 0.1363 0.1805 0.1747 random, 5% 19.9
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] -0.1296 -1.4325 -1.3972 1.5268
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.562 f_angle_d 1.147 f_chiral_restr 0.08 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6937 Nucleic Acid Atoms Solvent Atoms 1049 Heterogen Atoms 13
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 data collection HKL-3000 phasing MOLREP phasing PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling