2HBU

Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HBT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.4298200-300 mM (NH4)2SO4, 100 mM NaOAc pH 4.8-5.4, 22-25% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5752.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.045α = 90
b = 111.045β = 90
c = 40.126γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.853099.20.03118.74.62424824248
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.851.9595.70.362.952.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2HBT1.8532.532424322995123399.340.181290.17870.23082RANDOM32.709
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.549
r_dihedral_angle_4_deg21.107
r_dihedral_angle_3_deg18.376
r_dihedral_angle_1_deg10.088
r_scangle_it6.892
r_scbond_it5.005
r_mcangle_it3.518
r_mcbond_it2.566
r_angle_refined_deg1.344
r_symmetry_hbond_refined0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.549
r_dihedral_angle_4_deg21.107
r_dihedral_angle_3_deg18.376
r_dihedral_angle_1_deg10.088
r_scangle_it6.892
r_scbond_it5.005
r_mcangle_it3.518
r_mcbond_it2.566
r_angle_refined_deg1.344
r_symmetry_hbond_refined0.45
r_symmetry_vdw_refined0.377
r_nbtor_refined0.327
r_nbd_refined0.235
r_xyhbond_nbd_refined0.208
r_chiral_restr0.124
r_bond_refined_d0.012
r_gen_planes_refined0.007
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 AtomsNumber
Protein Atoms1823
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data scaling
AMoREphasing