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HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with MD-253
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, SITTING DROP 6.5 293 Sample: 19.0 mg/ml PHD2 (50 mM Tris.HCl pH 7.5), 1.0 mM MnCl2 and 1.2 mM compound. Reservoir: 1.88 M ammonium sulfate, 0.1 M MES pH 6.5 and 5-7% dioxoane (v/v). Cryo-protection: 30% v/v glycerol.
Crystal Properties Matthews coefficient Solvent content 3.2 61.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.456 α = 90 b = 103.018 β = 90 c = 196.028 γ = 90
Symmetry Space Group P 21 21 21
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 2011-05-06 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) 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 2.847 50 99.4 0.18 0.2 0.112 0.998 6.71 5.3 40604 48.4
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 2.85 2.95 99.6 0.71 0.482 1.81 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2G19 2.847 23.753 1.96 40524 2041 99.43 0.2382 0.2368 0.2396 0.266 0.2712 55.0728
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 16.442 f_angle_d 0.795 f_chiral_restr 0.048 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9117 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 271
Software Software Software Name Purpose HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing