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Structure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum at 1.35 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 6.4 293 14% PEG6000, 0.1M calcium chloride, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.42 49.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.485 α = 90 b = 152.089 β = 90 c = 96.188 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 CCD MARMOSAIC 225 mm CCD 2008-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
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 1.35 48.094 96.1 0.094 0.104 0.045 11.3 5.2 338753 338753
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 1.35 1.42 93 0.769 0.769 0.366 1 5 47581
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 1.35 48.09 321788 16910 95.94 0.1135 0.1121 0.1121 0.1397 0.1398 RANDOM 12.958
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] 0.03 -0.07 0.04
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 27.05 r_sphericity_bonded 7.576 r_rigid_bond_restr 1.98 r_angle_refined_deg 1.369 r_mcangle_it 1.209 r_mcbond_it 0.969 r_mcbond_other 0.967 r_angle_other_deg 0.796 r_chiral_restr 0.088 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 27.05 r_sphericity_bonded 7.576 r_rigid_bond_restr 1.98 r_angle_refined_deg 1.369 r_mcangle_it 1.209 r_mcbond_it 0.969 r_mcbond_other 0.967 r_angle_other_deg 0.796 r_chiral_restr 0.088 r_bond_refined_d 0.009 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 11600 Nucleic Acid Atoms Solvent Atoms 1968 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing