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Crystal Structure of BphD, a C-C hydrolase from Burkholderia xenovorans LB400
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.2 293 2.0-2.4 M ammonium sulfate, 6-10% ethanol, 0.1M Tris-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.75 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135 α = 90 b = 135 β = 90 c = 66.725 γ = 120
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 ADSC QUANTUM 1 1998-09-18 M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC QUANTUM 1 1998-12-05 M MAD 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D APS 14-BM-D 2 SYNCHROTRON APS BEAMLINE 14-BM-D 0.9537,0.9793,0.9795 APS 14-BM-D
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 1.6 50 96.6 0.06 9.9 88125
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 1.6 1.63 74.1 0.36 3352
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.6 19.87 88125 8856 96.6 0.208 0.2107 0.224 0.2264 RANDOM 27.1
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] 0.32 1.25 0.32 -0.64
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.1 c_scangle_it 2.72 c_mcangle_it 1.77 c_scbond_it 1.76 c_angle_deg 1.2 c_mcbond_it 1.12 c_improper_angle_d 0.7 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4492 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 35
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing CNS refinement PDB_EXTRACT data extraction ADSC data collection