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HIF prolyl-hydroxylase-2 (PHD2) T387V variant bound to Fe(III), 2-oxoglutarate (2OG) and Hypoxia-inducible Factor-2alpha (HIF-2alpha)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PHD2 bound to HIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 296 (10-35%) PEG 4K, 0.2 M ammonium acetate and 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6).
Crystal Properties Matthews coefficient Solvent content 1.95 36.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.24 α = 90 b = 38.34 β = 90 c = 42.98 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 2022-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.62 42.98 98.9 1 15.9 12.4 26767 25.28
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 1.62 1.65 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 1.62 42.98 1.34 26710 1333 93.8 0.1918 0.1904 0.1918 0.219 0.2169 31.37
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 7.6953 f_angle_d 0.6568 f_chiral_restr 0.046 f_plane_restr 0.0064 f_bond_d 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1839 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 15
Software Software Software Name Purpose PHENIX refinement PHENIX refinement xia2 data reduction d*TREK data scaling PHASER phasing