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Crystal Structure of the Biphenyl Dioxygenase from Comamonas testosteroni Sp. Strain B-356
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NDO PDB ENTRY 1NDO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 20-15% PEG 4000, 100mM MES, 10-15% 2-PROPANOL, SODIUM CHLORIDE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.59 52.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.233 α = 90 b = 136.233 β = 90 c = 106.237 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 0.9 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.62 50 99.4 0.067 0.067 13 2.9 91600 91600 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.69 99.4 0.194 0.194 5.5 2.9
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB ENTRY 1NDO 1.62 39.33 91600 91600 93.5 0.118 0.2778 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 12 5520.45
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.064 s_non_zero_chiral_vol 0.061 s_zero_chiral_vol 0.052 s_from_restr_planes 0.03 s_angle_d 0.029 s_anti_bump_dis_restr 0.018 s_bond_d 0.012 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5023 Nucleic Acid Atoms Solvent Atoms 580 Heterogen Atoms 17
Software Software Software Name Purpose HKL-2000 data collection SHELX model building SHELXL-97 refinement HKL-2000 data reduction SCALEPACK data scaling SHELX phasing