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Structure of H200C variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with HPCA at 1.46 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 13-15% PEG6K, 0.1M calcium chloride, 0.1M MOPS
Crystal Properties Matthews coefficient Solvent content 2.41 48.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.414 α = 90 b = 151.027 β = 90 c = 96.468 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 0.9763 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 1.46 29.7 96.9 0.059 0.068 0.034 12.3 3.8 269165 269165
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 1.46 1.54 94 0.71 0.71 0.409 2 3.8 37792
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 1.46 29.66 255730 13391 96.69 0.1236 0.1217 0.1605 0.1676 RANDOM 20.44
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] 0.16 -0.1 -0.06
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 25.746 r_sphericity_bonded 9.969 r_rigid_bond_restr 2.408 r_mcangle_it 2.17 r_mcbond_it 1.904 r_mcbond_other 1.898 r_angle_refined_deg 1.301 r_angle_other_deg 0.789 r_chiral_restr 0.087 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 25.746 r_sphericity_bonded 9.969 r_rigid_bond_restr 2.408 r_mcangle_it 2.17 r_mcbond_it 1.904 r_mcbond_other 1.898 r_angle_refined_deg 1.301 r_angle_other_deg 0.789 r_chiral_restr 0.087 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 11555 Nucleic Acid Atoms Solvent Atoms 1506 Heterogen Atoms 126
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing