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Crystal Structure of Biphenyl 2,3-Dioxygenase from Sphingomonas yanoikuyae B1
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, HANGING DROP 6.8 277.15 20% PEG3350, 1.0 M Sodium Chloride, 0.037M Zinc Chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.68 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.958 α = 90 b = 134.958 β = 90 c = 219.887 γ = 120
Symmetry Space Group P 31 2 1
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 2004-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID
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 1.7 19.8 95.3 0.083 8.2 4.48 253570 241600
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 1.7 1.76 98.1 0.394 2.9 4.1
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 1NDO 1.7 19.8 253570 229247 12180 95.22 0.19012 0.1881 0.199 0.2283 0.237 RANDOM 28.962
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] 0.02 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.181 r_dihedral_angle_4_deg 15.322 r_dihedral_angle_3_deg 13.986 r_dihedral_angle_1_deg 6.845 r_scangle_it 3.476 r_scbond_it 2.544 r_angle_refined_deg 1.629 r_mcangle_it 1.527 r_mcbond_it 1.312 r_angle_other_deg 0.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.181 r_dihedral_angle_4_deg 15.322 r_dihedral_angle_3_deg 13.986 r_dihedral_angle_1_deg 6.845 r_scangle_it 3.476 r_scbond_it 2.544 r_angle_refined_deg 1.629 r_mcangle_it 1.527 r_mcbond_it 1.312 r_angle_other_deg 0.968 r_mcbond_other 0.293 r_metal_ion_refined 0.237 r_symmetry_vdw_other 0.231 r_symmetry_hbond_refined 0.222 r_nbd_other 0.211 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.203 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.102 r_nbtor_other 0.085 r_xyhbond_nbd_other 0.041 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14987 Nucleic Acid Atoms Solvent Atoms 1978 Heterogen Atoms 21
Software Software Software Name Purpose d*TREK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction JDirector data collection