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HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with monocyclic BB-328
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 Sample: (20 mg/ml PHD2 + 1 mM FeSO4 + 2 mM compound); Reservoir: 1.6-2.0 M (NH4)2SO4, 2-8% dioxane, 0.1 M MES-Na pH 6.5, and 1 mM FeSO4; Hanging drop (2 ul), protein-to-well ratio, 1:1, 293K
Crystal Properties Matthews coefficient Solvent content 2.79 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.175 α = 90 b = 110.175 β = 90 c = 39.791 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 CCD RIGAKU SATURN 944 VARIMAX HF 2011-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.97 50 99.8 0.092 18.77 7.8 19800 36
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 1.97 2 99.6 0.915 2.38 7.2
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 THROUGHOUT 2G19 1.97 18.448 1.33 19658 1001 99.38 0.1881 0.187 0.1879 0.2081 0.2115 59.1114
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 16.605 f_angle_d 1.439 f_chiral_restr 0.074 f_bond_d 0.017 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1727 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing