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HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with N-oxalylglycine (NOG) and a RaPID-derived silent allosteric cyclic peptide 3C (14-mer)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Sample: 1.0 mM cPHD2, 1.5 mM MnCl2, 2.0 mM compound, 1.0 mM 3C; Reservoir: 0.2 M lithium sulfate, 0.1 M Tris-HCl pH 8.5, 1.26 M ammonium sulfate; Sitting drop (300 nl), protein-to-well ratio, 1:1
Crystal Properties Matthews coefficient Solvent content 2.56 51.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.622 α = 90 b = 46.622 β = 90 c = 203.711 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 PIXEL DECTRIS PILATUS 6M-F MIRRORS 2015-09-17 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) Rrim I (All) Rpim I (All) 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 1.528 50 100 0.124 0.129 0.039 0.996 20.07 16 37807 21.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.58 100 0.532 0.653 1.73 13.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5L9R 1.528 39.605 1.35 37652 1841 99.7 0.1628 0.162 0.1656 0.177 0.1799 34.4686
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 11.882 f_angle_d 1.407 f_chiral_restr 0.087 f_bond_d 0.016 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1756 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 24
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing