2G19 | pdb_00002g19

Cellular Oxygen Sensing: Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.429828% polyethylene glycol 8000, 0.2 M ammonium sulfate, 100 mM MES buffer with 10 fold molar excess of inhibitor, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.40
Crystal Properties
Matthews coefficientSolvent content
2.652.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.851α = 90
b = 110.851β = 90
c = 40.379γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 42005-12-14MSINGLE WAVELENGTH
21x-rayM
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1,21.74897.90.07932103080421.7
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)
1.71.7393.60.51325

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONCOMBINED MAD AND SIRASTHROUGHOUT1.7483012930129242195.60.2160.253RANDOM29.2
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]
-1.31-0.05-1.312.62
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.9
c_angle_deg1.5
c_improper_angle_d0.87
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.9
c_angle_deg1.5
c_improper_angle_d0.87
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1708
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms20

Software

Software
Software NamePurpose
ALS5.0.2data collection
SCALEPACKdata scaling
SOLVEphasing
CNXrefinement