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Biphenyl-2,3-diol-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 2.62 53.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.257 α = 90 b = 89.793 β = 103.99 c = 105.445 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 PIXEL DECTRIS PILATUS 2M-F 2018-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 1.79 50 99.9 0.082 24 6.9 121104
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 2 2.03 0.876
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 1.99 36.59 113684 6097 98.66 0.1643 0.162 0.1717 0.207 0.2136 RANDOM 30.155
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] -0.09 -0.18 0.03 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.503 r_dihedral_angle_4_deg 19.555 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_1_deg 7.077 r_angle_refined_deg 1.599 r_angle_other_deg 0.931 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.503 r_dihedral_angle_4_deg 19.555 r_dihedral_angle_3_deg 14.555 r_dihedral_angle_1_deg 7.077 r_angle_refined_deg 1.599 r_angle_other_deg 0.931 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11722 Nucleic Acid Atoms Solvent Atoms 1040 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing