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Crystal structure of human Transmembrane prolyl 4-hydroxylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 Well solution: 0.1 M Tris-HCl pH 9, 22% Tert-butanol, 1 mM N-oxalylglycine
Protein solution: 10 mM Tris-HCl pH 7.8, 0.1 M NaCl, 0.1 M Glycine, 2 mM CaCl2, 0.02 mM FeSO4
Crystal Properties Matthews coefficient Solvent content 3.4 62.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.079 α = 90 b = 92.079 β = 90 c = 129.5 γ = 120
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 2018-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.25 50.3 98 0.092 0.109 0.057 0.995 7.35 3.4 57041 60.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 83 1.95 2.38 1.34 0.18 0.4 2.7
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 2jig 2.25 50.3 1.92 57031 2008 98 0.1829 0.1815 0.1876 0.2213 0.2227 87.78
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 9.5652 f_angle_d 0.6964 f_chiral_restr 0.0443 f_bond_d 0.0048 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5874 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 366
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing Coot model building