5A3U

HIF prolyl hydroxylase 2 (PHD2/EGLN1) in complex with 6-(5-oxo-4-(1H- 1,2,3-triazol-1-yl)-2,5-dihydro-1H-pyrazol-1-yl)nicotinic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BQYPDB ENTRY 4BQY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52931.6 M SODIUM CITRATE/CITRIC ACID PH 6.5, SITTING DROP, 293K
Crystal Properties
Matthews coefficientSolvent content
3.5164.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.939α = 90
b = 154.939β = 90
c = 85.401γ = 120
Symmetry
Space GroupP 32 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MMIRRORS2012-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
13.344.7399.20.226.76.117598271.57
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)
13.33.4899.90.881.95.8

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4BQY3.344.7271.351756689499.10.19160.20230.226663.5
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]
8.258.25-16.5
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.024
f_angle_d0.975
f_chiral_restr0.032
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4697
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms63

Software

Software
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing