8Z33 | pdb_00008z33

Crystal Structure of HIF-PHD2 in complex with compound 4


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION295Protein (30mg/ml in 20mM Tril-HCl (pH 7.5), 50mM NaCl), reservoir solution (1.3M ammonium sulfate, 0.1M NaCl, 0.05M NaF, 0.1M HEPES (pH 7.5))
Crystal Properties
Matthews coefficientSolvent content
2.2946.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.816α = 90
b = 88.747β = 96.35
c = 70.762γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-11-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A

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
12.65099.10.06314.93.715274
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)
12.62.66930.3352.93.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.62013750147698.590.206270.201650.21250.248810.2585RANDOM65.97
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]
3.711.57-1.05-2.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.02
r_long_range_B_refined8.76
r_dihedral_angle_2_deg7.587
r_dihedral_angle_1_deg6.249
r_mcangle_it4.314
r_scbond_it3.631
r_mcbond_it2.629
r_angle_refined_deg1.006
r_chiral_restr0.08
r_bond_refined_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.02
r_long_range_B_refined8.76
r_dihedral_angle_2_deg7.587
r_dihedral_angle_1_deg6.249
r_mcangle_it4.314
r_scbond_it3.631
r_mcbond_it2.629
r_angle_refined_deg1.006
r_chiral_restr0.08
r_bond_refined_d0.003
r_gen_planes_refined0.003
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 AtomsNumber
Protein Atoms3318
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing