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Structure of H200E variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-nitrocatechol at 1.48 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 acetate, 0.1M MOPS
Crystal Properties Matthews coefficient Solvent content 2.39 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.268 α = 90 b = 150.875 β = 90 c = 95.919 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 2011-12-07 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 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 1.48 45.7 99.2 0.061 0.069 0.031 14.6 4.5 262655 262655
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 1.48 1.56 99.4 0.835 0.835 0.425 0.9 4.4 38167
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3OJT 1.48 45.7 249494 13081 99.02 0.1196 0.1174 0.1621 0.1625 RANDOM 20.301
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] 0.05 -0.17 0.12
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 30.001 r_sphericity_bonded 10.921 r_rigid_bond_restr 3.296 r_mcangle_it 2.54 r_mcbond_it 2.258 r_mcbond_other 2.258 r_angle_refined_deg 1.469 r_angle_other_deg 0.828 r_chiral_restr 0.097 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 30.001 r_sphericity_bonded 10.921 r_rigid_bond_restr 3.296 r_mcangle_it 2.54 r_mcbond_it 2.258 r_mcbond_other 2.258 r_angle_refined_deg 1.469 r_angle_other_deg 0.828 r_chiral_restr 0.097 r_bond_refined_d 0.012 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 11510 Nucleic Acid Atoms Solvent Atoms 1623 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing