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Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2) with (S)-{2-[2-(5-Cyano-3-hydroxy-pyridin-2-yl)-thiazol-4-yl]-acetylamino}-phenyl-acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HBU PDB entry 2HBU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 295 0.1M HEPES, 35% PEG8K, 0.2M ammonium sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.25 45.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.207 α = 90 b = 72.207 β = 90 c = 46.01 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315r 2009-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 4A PAL/PLS 4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.15 50 100 0.072 0.06 31.48 4.8 13128 22.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 100 0.429 0.377 3.31 4.6 12187
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 2HBU 2.15 34.18 13085 12556 640 95.9 0.211 0.211 0.2236 0.23 0.2386 RANDOM 48.6
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] -4.63 -4.63 9.26
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 3.31 c_mcangle_it 2.78 c_scbond_it 2.19 c_mcbond_it 1.62 c_angle_deg 1.2 c_improper_angle_d 0.76 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1826 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 44
Software Software Software Name Purpose HKL-2000 data collection PHASES phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling