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Taurine/alpha-ketoglutarate Dioxygenase from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQW PDB ENTRY 1GQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20-28% PEG1000, 20% ETHYLENE GLYCOL, 75MM IMIDAZOLE PH7.5, PROTEIN SOLUTION LOADED WITH FE(II), ALPHA-KETOGLUTARATE, TAURINE, DITHIOTHREITOL, pH 7.50
Crystal Properties Matthews coefficient Solvent content 3 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.786 α = 90 b = 116.786 β = 90 c = 201.937 γ = 120
Symmetry Space Group P 62 2 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 MARRESEARCH 1998-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.5 90 99.3 0.069 7.4 8 28679
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 2.5 2.64 99.1 0.311 2.3 7.8
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 PDB ENTRY 1GQW 2.5 45.18 25742 2840 99.3 0.264 0.261 0.2759 0.293 0.3012 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.449 r_scbond_it 2.132 r_angle_other_deg 2.045 r_mcangle_it 1.218 r_dihedral_angle_3_deg 1.021 r_mcbond_it 0.687 r_symmetry_vdw_refined 0.372 r_symmetry_vdw_other 0.297 r_symmetry_hbond_refined 0.26 r_nbd_refined 0.246
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 3.449 r_scbond_it 2.132 r_angle_other_deg 2.045 r_mcangle_it 1.218 r_dihedral_angle_3_deg 1.021 r_mcbond_it 0.687 r_symmetry_vdw_refined 0.372 r_symmetry_vdw_other 0.297 r_symmetry_hbond_refined 0.26 r_nbd_refined 0.246 r_nbd_other 0.235 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.132 r_nbtor_other 0.107 r_xyhbond_nbd_other 0.1 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4357 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling