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Crystal Structure of a Prolyl 4-Hydroxylase Complexed with Alpha-ketoglutarate from the Pathogenic Bacterium Bacillus anthracis in C2221
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ITQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 293 0.1 M HEPES pH 7.8, 0.05 M Cadmium sulfate, 0.9 M Sodium acetate tri-hydrate, 0.1 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.36 47.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.551 α = 90 b = 146.189 β = 90 c = 75.075 γ = 90
Symmetry Space Group C 2 2 21
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 NOIR-1 2014-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.35 52.372 99.9 0.098 15.8 7 10150 24.68
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 2.35 2.48 99.9 0.377 1.9 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ITQ 2.35 52.37 1.34 10133 495 99.9 0.201 0.199 0.1992 0.245 0.246
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 f_dihedral_angle_d 15.123 f_angle_d 0.518 f_chiral_restr 0.042 f_bond_d 0.006 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1517 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing