4QTD

Structure of human JNK1 in complex with SCH772984 and the AMPPNP-hydrolysed triphosphate revealing the second type-I binding mode


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YDIpdb entry 2YDI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.1512-15% PEG3350 and 0.1 M HEPES pH 6.8-7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties
Matthews coefficientSolvent content
2.3447.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.95α = 90
b = 71.55β = 90
c = 108.17γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MKirkpatrick Baez bimorph mirror pair2014-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97625DiamondI04

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
11.525.7599.90.06414.96.4640416396915.2
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)
11.51.5899.40.4973.14.99131

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)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 2YDI1.559.6826396960781318799.850.166920.16560.19211RANDOM24.467
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]
0.48-0.14-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.269
r_dihedral_angle_4_deg18.88
r_dihedral_angle_3_deg13.564
r_long_range_B_refined6.992
r_long_range_B_other6.991
r_dihedral_angle_1_deg6.085
r_scangle_other3.548
r_scbond_it2.483
r_scbond_other2.481
r_mcangle_other2.243
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.269
r_dihedral_angle_4_deg18.88
r_dihedral_angle_3_deg13.564
r_long_range_B_refined6.992
r_long_range_B_other6.991
r_dihedral_angle_1_deg6.085
r_scangle_other3.548
r_scbond_it2.483
r_scbond_other2.481
r_mcangle_other2.243
r_mcangle_it2.242
r_angle_refined_deg1.613
r_mcbond_other1.415
r_mcbond_it1.414
r_angle_other_deg0.802
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2871
Nucleic Acid Atoms
Solvent Atoms367
Heterogen Atoms161

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling