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Crystal Structure of the S112A/H265A double mutant of a C-C hydrolase, BphD from Burkholderia xenovorans LB400, in complex with its substrate HOPDA
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 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.805 α = 90 b = 116.805 β = 90 c = 87.528 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 2005-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.00 APS 21-ID-D
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 82.5 99.1 8.8 21.2 9.3 42069 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 1.57 1.61 99.1 45.8 3.5 6.9
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 1.57 82.48 39930 39930 2123 99.12 0.17627 0.1749 0.1808 0.20234 0.2115 RANDOM 24.286
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] 0.44 0.44 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.5 r_dihedral_angle_4_deg 16.069 r_dihedral_angle_3_deg 13.542 r_scangle_it 12.483 r_scbond_it 9.4 r_dihedral_angle_1_deg 5.274 r_mcangle_it 5.109 r_mcbond_it 3.519 r_angle_refined_deg 1.21 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.5 r_dihedral_angle_4_deg 16.069 r_dihedral_angle_3_deg 13.542 r_scangle_it 12.483 r_scbond_it 9.4 r_dihedral_angle_1_deg 5.274 r_mcangle_it 5.109 r_mcbond_it 3.519 r_angle_refined_deg 1.21 r_nbtor_refined 0.306 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.182 r_metal_ion_refined 0.163 r_xyhbond_nbd_refined 0.103 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2234 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing