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Crystal structure of 2,3-dihydroxybiphenyal dioxygenase (BphC) at 1.45 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Batch method 7.5 285 Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch method, temperature 285K
Crystal Properties Matthews coefficient Solvent content 3.14 60.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.76 α = 90 b = 121.76 β = 90 c = 108.91 γ = 90
Symmetry Space Group I 4 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 ADSC QUANTUM 4 2000-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0 Photon Factory BL-6A
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 1.45 20.29 99.9 0.081 0.081 5 11.7 72106 72066
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 1.45 1.53 99.9 0.393 0.393 1.9 9.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.45 87.71 68425 68425 3641 99.87 0.16213 0.16213 0.16137 0.1708 0.17653 0.1846 RANDOM 11.583
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.131 r_dihedral_angle_1_deg 5.131 r_scangle_it 2.792 r_sphericity_free 2.198 r_scbond_it 1.72 r_angle_other_deg 1.571 r_angle_refined_deg 1.439 r_mcangle_it 1.194 r_symmetry_hbond_refined 0.707 r_mcbond_it 0.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.131 r_dihedral_angle_1_deg 5.131 r_scangle_it 2.792 r_sphericity_free 2.198 r_scbond_it 1.72 r_angle_other_deg 1.571 r_angle_refined_deg 1.439 r_mcangle_it 1.194 r_symmetry_hbond_refined 0.707 r_mcbond_it 0.658 r_symmetry_vdw_other 0.302 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.21 r_nbtor_other 0.203 r_nbd_other 0.196 r_xyhbond_nbd_other 0.14 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2229 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 17
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling