4BQW

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Mn(II) and 2-(4-hydroxy-2-oxo-1,2-dihydroquinoline-3-carboxamido)acetic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G19PDB ENTRY 2G19

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1M MES PH6.5, 1.7M AMMONIUM SULFATE, 1% DIOXANE, 0.002M MNCL2, SITTING DROP, 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.914α = 90
b = 109.914β = 90
c = 39.409γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944VARIMAX HF2011-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT

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
11.7923.898.90.0622.45.32570526.2
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)
11.791.8599.90.682.053.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2G191.7923.825560130498.90.1950.1950.201RANDOM35.5
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]
-1.39-1.392.78
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.6
c_scangle_it2.62
c_mcangle_it2.26
c_scbond_it1.78
c_angle_deg1.5
c_mcbond_it1.39
c_improper_angle_d0.95
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.6
c_scangle_it2.62
c_mcangle_it2.26
c_scbond_it1.78
c_angle_deg1.5
c_mcbond_it1.39
c_improper_angle_d0.95
c_bond_d0.006
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1671
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms21

Software

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