6YW0

Lysine-N,N-Dimethylated HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with BB-287


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G19 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Sample: 18 mg/mL PHD2-Me + 1 mM FeSO4 + 2 mM compound; Reservoir: 1.7% polyethylene glycol 400, 15% glycerol, 1.7 M ammonium sulphate and 0.085 M HEPES-Na pH 7.5; Sitting drop (2 uL), protein-to-well ratio, 1:1
Crystal Properties
Matthews coefficientSolvent content
3.0960.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.927α = 90
b = 110.927β = 90
c = 39.66γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDPT COATED MIRRORS IN A KIRKPATRICK-BAEZ (KB) GEOMETRY2006-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87260ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.236.30999.90.1770.1820.0419.120.3144271442741
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.321002.0372.0372.0880.4551.7420.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 REPLACEMENTTHROUGHOUT2G192.232.0221.331441372399.920.19370.19230.220871.7747
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d9.594
f_angle_d0.851
f_chiral_restr0.051
f_plane_restr0.005
f_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1743
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms35

Software

Software
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing