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Crystal Structure of the S112A mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with 3-Cl 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 2.37 48.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.774 α = 90 b = 117.774 β = 90 c = 86.739 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 2005-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 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 1.7 83.33 99.56 6.6 29.7 9.8 33456 2 2 20.3
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 1.7 1.76 100 49.2 3.3 9.3 3297
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 1.7 83.33 33453 1692 99.56 0.154 0.153 0.1579 0.189 0.198 RANDOM 21.065
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] 0.2 0.2 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.884 r_dihedral_angle_4_deg 16.846 r_dihedral_angle_3_deg 13.143 r_scangle_it 10.826 r_scbond_it 8.673 r_mcangle_it 5.337 r_dihedral_angle_1_deg 5.314 r_mcbond_it 3.706 r_angle_refined_deg 1.22 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.884 r_dihedral_angle_4_deg 16.846 r_dihedral_angle_3_deg 13.143 r_scangle_it 10.826 r_scbond_it 8.673 r_mcangle_it 5.337 r_dihedral_angle_1_deg 5.314 r_mcbond_it 3.706 r_angle_refined_deg 1.22 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.21 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.182 r_metal_ion_refined 0.151 r_xyhbond_nbd_refined 0.13 r_symmetry_metal_ion_refined 0.094 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2239 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 25
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling