4FVP

Crystal structure of the Jak2 pseudokinase domain (apo form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M14PDB ENTRY 1M14

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8277100 mM Tris/HCl, PEG 4000, pH 8.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1743.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.362α = 90
b = 57.143β = 110.42
c = 60.996γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic Blue2011-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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
12.015099.80.03923.53.719131
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)
12.012.0898.60.1213.51857

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 1M142.0133.61909098199.560.18130.17960.2123RANDOM25.6472
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]
1.460.02-0.48-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.583
r_dihedral_angle_4_deg19.222
r_dihedral_angle_3_deg13.19
r_dihedral_angle_1_deg5.856
r_angle_refined_deg1.198
r_angle_other_deg0.799
r_chiral_restr0.069
r_bond_refined_d0.007
r_bond_other_d0.006
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.583
r_dihedral_angle_4_deg19.222
r_dihedral_angle_3_deg13.19
r_dihedral_angle_1_deg5.856
r_angle_refined_deg1.198
r_angle_other_deg0.799
r_chiral_restr0.069
r_bond_refined_d0.007
r_bond_other_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2140
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms12

Software

Software
Software NamePurpose
d*TREKdata scaling
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction
HKL-2000data scaling