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HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in complex with tert-butyl 6-(5-hydroxy-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-1-yl)nicotinate (IOX4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.15M Potassium thiocyanate pH 7, 20.5% PEG 3350, Sitting Drop (300 nL), protein-to-well ratio, 2:1, 298K
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.062 α = 90 b = 75.472 β = 95.04 c = 127.555 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 X 16M 2019-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.01 76.76 99.9 0.063 0.024 13.3 6.8 97320 46.843
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.04 98.8 1.874 0.726 1 6.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HQR 2.01 19.97 1.34 96952 4821 99.69 0.2064 0.2052 0.2299 0.2315 74.1576
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9348 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 259
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHASER phasing Coot model building MolProbity model building PDB_EXTRACT data extraction