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Crystal structure of 2,3-dihydroxybiphenyl dioxygenase (BphC) in complex with 2,3-dihydroxybiphenyl at 2.0A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Batch 7.5 285 Tris/HCl, hexylene glycol, Ammonium Sulfate, pH 7.5, Batch, temperature 285K
Crystal Properties Matthews coefficient Solvent content 3.13 60.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.629 α = 90 b = 121.629 β = 90 c = 108.753 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 2000-02-05 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) 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 1.939 28.67 93.5 0.064 9.8 28896 28532 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.04 93.5
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 (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 1.95 84.51 28531 27080 1451 94.42 0.1619 0.16076 0.1746 0.1833 0.2003 RANDOM 17.174
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] -0.11 -0.11 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.547 r_dihedral_angle_1_deg 3.663 r_scangle_it 2.835 r_scbond_it 1.709 r_angle_refined_deg 1.279 r_mcangle_it 1.135 r_symmetry_hbond_refined 0.931 r_angle_other_deg 0.721 r_mcbond_it 0.604 r_symmetry_vdw_other 0.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.547 r_dihedral_angle_1_deg 3.663 r_scangle_it 2.835 r_scbond_it 1.709 r_angle_refined_deg 1.279 r_mcangle_it 1.135 r_symmetry_hbond_refined 0.931 r_angle_other_deg 0.721 r_mcbond_it 0.604 r_symmetry_vdw_other 0.223 r_nbd_other 0.2 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.133 r_symmetry_vdw_refined 0.092 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_xyhbond_nbd_other 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbtor_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2229 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 15
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling AMoRE phasing REFMAC refinement CCP4 data scaling