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Crystal Structure of HIF-PHD2 in complex with compound 3-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HBT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 Protein (30mg/ml in a final buffer of 20mM Tril-HCl (pH 7.5), 50mM NaCl), Reservoir solution (30% (w/v) PEG MME 5000, 0.2M ammonium sulfate, 0.1M HEPES (pH 7.0))
Crystal Properties Matthews coefficient Solvent content 2.29 46.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.435 α = 90 b = 71.435 β = 90 c = 45.493 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 100 IMAGE PLATE RIGAKU 2007-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E 1.5418
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 1.8 50 96.7 0.029 26.1 3.6 20794
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 1.8 1.86 95.2 0.075 10.1 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.8 19.82 18627 2157 96.79 0.2011 0.19771 0.2219 0.22993 0.2444 RANDOM 17.185
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] -0.2 -0.2 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.919 r_dihedral_angle_1_deg 6.441 r_long_range_B_refined 4.958 r_dihedral_angle_2_deg 4.565 r_scbond_it 1.794 r_mcangle_it 1.501 r_angle_refined_deg 1.244 r_mcbond_it 0.984 r_chiral_restr 0.09 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.919 r_dihedral_angle_1_deg 6.441 r_long_range_B_refined 4.958 r_dihedral_angle_2_deg 4.565 r_scbond_it 1.794 r_mcangle_it 1.501 r_angle_refined_deg 1.244 r_mcbond_it 0.984 r_chiral_restr 0.09 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1714 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing PDB_EXTRACT data extraction