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Structure of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol at 1.55 Ang resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl. Cryoprotectant 25% PEG400. Ligand soaking: 2mM 4-nitrocatechol for 1.5 hours in anaerobic glovebox atmosphere prior to cryo-cooling in liquid nitrogen., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.246 α = 90 b = 150.509 β = 90 c = 96.243 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M 2012-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9801 SOLEIL PROXIMA 1
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 1.55 48.1 99.9 0.037 12.1 5.9 231042 231042 -3
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 1.55 1.63 99.8 0.413 2 5.3 33407
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 3OJT 1.55 47.83 219459 11502 99.84 0.12534 0.12326 0.1243 0.16466 0.1644 RANDOM 19.231
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 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.79 r_sphericity_free 27.018 r_dihedral_angle_4_deg 18.032 r_dihedral_angle_3_deg 12.239 r_sphericity_bonded 9.753 r_dihedral_angle_1_deg 7.07 r_rigid_bond_restr 2.936 r_angle_refined_deg 1.477 r_angle_other_deg 0.928 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.79 r_sphericity_free 27.018 r_dihedral_angle_4_deg 18.032 r_dihedral_angle_3_deg 12.239 r_sphericity_bonded 9.753 r_dihedral_angle_1_deg 7.07 r_rigid_bond_restr 2.936 r_angle_refined_deg 1.477 r_angle_other_deg 0.928 r_chiral_restr 0.098 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 11556 Nucleic Acid Atoms Solvent Atoms 1594 Heterogen Atoms 146
Software Software Software Name Purpose MX data collection REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing