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Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.05 M Bis-Tris pH 5.5
0.1 M Ammonium Acetate
12.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.61 52.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.294 α = 90 b = 89.684 β = 104.08 c = 105.021 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315 2018-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.74 200 100 0.089 22.1 6.9 131252
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.97 0.789
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2DE5 1.93 44.88 120993 6252 96.34 0.1603 0.1583 0.1674 0.2002 0.2063 RANDOM 24.034
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.069 r_dihedral_angle_4_deg 17.127 r_dihedral_angle_3_deg 14.124 r_dihedral_angle_1_deg 7.324 r_angle_refined_deg 1.689 r_angle_other_deg 1.357 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.069 r_dihedral_angle_4_deg 17.127 r_dihedral_angle_3_deg 14.124 r_dihedral_angle_1_deg 7.324 r_angle_refined_deg 1.689 r_angle_other_deg 1.357 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11715 Nucleic Acid Atoms Solvent Atoms 1297 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing