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HIF prolyl hydroxylase 2 (PHD2-R281C/V314C) cross-linked to HIF-1alpha NODD-L397C/D412C and N-oxalylglycine (NOG) (complex-2)
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 7.5 293 0.1 M HEPES pH 7.5, 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.04 59.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.467 α = 90 b = 97.329 β = 90 c = 71.001 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 CCD ADSC QUANTUM 315r MIRRORS 2011-11-04 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) R Merge I (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 2.81 48.129 98.5 0.245 0.993 4.7769 3.4 15152 38
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 2.81 2.9 99.3 1.25 1.7378 3.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HQR 2.813 48.129 1.35 15094 717 97.7 0.2525 0.2513 0.2596 0.2785 0.2804 RANDOM 37.7
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] 19.42 -4.43 -14.98
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.175 f_angle_d 0.612 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3429 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing