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Crystal structure of Beta-lactamase from Burkholderia vietnamiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Morpheus Screen E8: 0.12 M Ethylene Glycols (equimolar mix of di- tri- tetra- and penta-ethylene glycol) 0.1M Buffer System 2 pH 7.5 (Na Hepes and MOPS acid), 50% Precipitant mix 4 (25% MPD, 25% PEG1000, 25% PEG3350); BuamA.00078.a.B1.PS02512 at 52.5 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.21 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.5 α = 90 b = 63.31 β = 90 c = 99.18 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 CCD RIGAKU SATURN 944+ 2015-01-20 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) 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 1.8 39.04 100 0.053 0.056 0.999 30.59 9.7 24922 -3 17.02
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 1.8 1.85 99.9 0.524 0.576 0.896 3.56
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 3W4Q 1.8 39.04 1.34 24921 2147 99.95 0.1567 0.1532 0.1535 0.195 0.1951 21.2123
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 17.228 f_angle_d 0.927 f_chiral_restr 0.062 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1878 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction