☰ Navigation Tabs
prolyl hydroxylase in complex with hypoxia inducible factor oxygen degradation domain peptide fragment from Trichoplax adhaerens
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 5.5 293 20 mg/ml protein, 1mM MN(II)CL2, 2mM N-oxalylglycine, 10mM taHIF-ODD peptide, 0.31M ammonium acetate, 24% (w/v) PEG3350, 0.1M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 1.82 0.325
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.841 α = 114.06 b = 41.321 β = 95.67 c = 42.076 γ = 103.69
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 315 MIRRORS 2010-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
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 1.3 50 95.1 0.112 8.5 6.8 55428 13.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 92.3 4.1
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 1.301 37.478 1.96 55413 2773 94.78 0.1389 0.1377 0.1481 0.1622 0.1689 RANDOM 20.6766
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 13.687 f_angle_d 1.157 f_chiral_restr 0.081 f_bond_d 0.012 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1853 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement GDA data collection DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction