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Mechanistic and Structural Analysis of Substrate Recognition and Cofactor Binding by an Unusual Bacterial Prolyl Hydroxylase - Co-BaP4H-PPG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.15 M KBr, 30 % PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 1.99 38.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.791 α = 90 b = 75.553 β = 90 c = 105.768 γ = 90
Symmetry Space Group P 21 21 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 2016-01-14 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) 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 2.1 61.479 99.8 0.068 0.088 0.041 13.1 4.6 24447 24447 29
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 2.1 2.21 100 0.496 1.4 4.4
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 5IAT 2.1 61.479 1.33 44894 2271 97.81 0.1985 0.1966 0.2008 0.234 0.2377 31.0923
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 19.209 f_angle_d 1.082 f_chiral_restr 0.066 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3063 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 33
Software Software Software Name Purpose SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction