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Aerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with Fe(III), 2-oxoglutarate (2OG) and HIF2alpha-CODD peptide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 (10-35%) PEG 4K, 0.2 M ammonium acetate , 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6)
Crystal Properties Matthews coefficient Solvent content 1.88 34.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.9 α = 90 b = 38.12 β = 90 c = 42.77 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M 2022-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9762 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.3 43.61 98.5 1 12.7 11.6 52821
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 0.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.37 42.77 1.33 45878 2299 99.77 0.181 0.1797 0.1821 0.2053 0.2072
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 6.516 f_angle_d 1.256 f_chiral_restr 0.094 f_plane_restr 0.016 f_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1818 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement DIALS data scaling xia2 data reduction PHASER phasing