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Crystal Structure of the S112A/H265Q mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSING, SITTING DROP, MICROSEEDING 6.8 298 2.4 M Sodium malonate, pH 6.8, VAPOR DIFFUSING, SITTING DROP, MICROSEEDING, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.458 α = 90 b = 117.458 β = 90 c = 87.791 γ = 90
Symmetry Space Group I 41 2 2
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 MARMOSAIC 300 mm CCD 2009-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B
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 2.11 83.06 97.8 0.126 7 7.6 17692
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 2.11 2.19 80.6 0.367 3.2 1432
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.11 83.06 17669 893 98.66 0.1809 0.1789 0.1836 0.2188 0.2244 RANDOM 24.0162
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] 0.74 0.74 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.636 r_dihedral_angle_4_deg 20.397 r_dihedral_angle_3_deg 14.554 r_dihedral_angle_1_deg 5.643 r_angle_refined_deg 1.261 r_angle_other_deg 0.861 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.636 r_dihedral_angle_4_deg 20.397 r_dihedral_angle_3_deg 14.554 r_dihedral_angle_1_deg 5.643 r_angle_refined_deg 1.261 r_angle_other_deg 0.861 r_chiral_restr 0.064 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2238 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling