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Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3,10-Di-Fluoro HOPDA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.9 M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.956 α = 90 b = 117.956 β = 90 c = 87.193 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 2007-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-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 1.57 50 99.6 8.1 20.2 11.2 42640 2 2 19.7
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 1.57 1.63 99.9 50.2 4.7 6.5 4205
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 1.57 27.8 42612 2151 99.48 0.173 0.171 0.1724 0.2 0.2027 RANDOM 23.159
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] 0.52 0.52 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.405 r_dihedral_angle_4_deg 19.468 r_dihedral_angle_3_deg 13.338 r_scangle_it 12.908 r_scbond_it 9.228 r_mcangle_it 6.323 r_dihedral_angle_1_deg 5.104 r_mcbond_it 3.854 r_angle_refined_deg 1.189 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.405 r_dihedral_angle_4_deg 19.468 r_dihedral_angle_3_deg 13.338 r_scangle_it 12.908 r_scbond_it 9.228 r_mcangle_it 6.323 r_dihedral_angle_1_deg 5.104 r_mcbond_it 3.854 r_angle_refined_deg 1.189 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.21 r_nbd_refined 0.205 r_metal_ion_refined 0.145 r_symmetry_metal_ion_refined 0.136 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.085 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2239 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction