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Crystal Structure of S112A/H265A double mutant of a C-C hydrolase, BphD, from Burkholderia xenovorans LB400
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OG1 PDB ENTRY 2OG1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.9 M sodium malonate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 100K, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.361 α = 90 b = 116.361 β = 90 c = 87.942 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 2006-07-05 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 2.07 82.2 98.8 8.4 23.9 9.3 18453 2 2
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 2.07 2.125 92.4 8.4 3 6.7 1697
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 (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 PDB ENTRY 2OG1 2.07 82.2 17503 18447 944 98.82 0.182 0.178 0.1856 0.258 0.2623 RANDOM 28.257
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] 1.21 1.21 -2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.761 r_scangle_it 17.546 r_scbond_it 16.841 r_dihedral_angle_4_deg 16.242 r_dihedral_angle_3_deg 15.993 r_mcangle_it 11.194 r_mcbond_it 10.29 r_dihedral_angle_1_deg 5.994 r_angle_refined_deg 1.592 r_symmetry_metal_ion_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.761 r_scangle_it 17.546 r_scbond_it 16.841 r_dihedral_angle_4_deg 16.242 r_dihedral_angle_3_deg 15.993 r_mcangle_it 11.194 r_mcbond_it 10.29 r_dihedral_angle_1_deg 5.994 r_angle_refined_deg 1.592 r_symmetry_metal_ion_refined 0.315 r_nbtor_refined 0.31 r_metal_ion_refined 0.266 r_nbd_refined 0.214 r_symmetry_vdw_refined 0.209 r_symmetry_hbond_refined 0.152 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.102 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2234 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 15
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing