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Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor
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, HANGING DROP 5.4 298 200-300 mM (NH4)2SO4, 100 mM NaOAc pH 4.8-5.4, 22-25% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.045 α = 90 b = 111.045 β = 90 c = 40.126 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 CCD MARRESEARCH 2005-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.85 30 99.2 0.031 18.7 4.6 24248 24248
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) 1.85 1.95 95.7 0.36 2.95 2.4
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 2HBT 1.85 32.53 24243 22995 1233 99.34 0.18129 0.1787 0.193 0.23082 0.2432 RANDOM 32.709
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.549 r_dihedral_angle_4_deg 21.107 r_dihedral_angle_3_deg 18.376 r_dihedral_angle_1_deg 10.088 r_scangle_it 6.892 r_scbond_it 5.005 r_mcangle_it 3.518 r_mcbond_it 2.566 r_angle_refined_deg 1.344 r_symmetry_hbond_refined 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.549 r_dihedral_angle_4_deg 21.107 r_dihedral_angle_3_deg 18.376 r_dihedral_angle_1_deg 10.088 r_scangle_it 6.892 r_scbond_it 5.005 r_mcangle_it 3.518 r_mcbond_it 2.566 r_angle_refined_deg 1.344 r_symmetry_hbond_refined 0.45 r_symmetry_vdw_refined 0.377 r_nbtor_refined 0.327 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.208 r_chiral_restr 0.124 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1823 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data scaling AMoRE phasing