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Structure of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-sulfonyl catechol at 1.52 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 7 293 14% PEG6000, 0.1M calcium chloride, 0.1M MOPS
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.399 α = 90 b = 151.247 β = 90 c = 96.158 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-F 2012-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.52 29.72 97.5 0.068 0.077 0.034 12 4.6 239601 239601
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.6 93.9 0.675 0.675 0.359 1.1 4.3 33400
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 1.52 29.51 227629 11922 97.19 0.1226 0.1206 0.1348 0.1609 0.1699 RANDOM 20.167
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] 0.1 -0.31 0.21
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 23.365 r_sphericity_bonded 9.116 r_rigid_bond_restr 2.73 r_mcangle_it 2.162 r_mcbond_it 1.938 r_mcbond_other 1.938 r_angle_refined_deg 1.289 r_angle_other_deg 0.793 r_chiral_restr 0.086 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 23.365 r_sphericity_bonded 9.116 r_rigid_bond_restr 2.73 r_mcangle_it 2.162 r_mcbond_it 1.938 r_mcbond_other 1.938 r_angle_refined_deg 1.289 r_angle_other_deg 0.793 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11532 Nucleic Acid Atoms Solvent Atoms 1392 Heterogen Atoms 167
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing