7NYK

SH3 domain of JNK-interacting Protein 1 (JIP1)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5293.150.1 M HEPES pH 7.5; 1-5 PEG 400; 2-2.5 M Ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.399α = 90
b = 82.128β = 90
c = 46.849γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.96546ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.3553.88391.80.9939.54.6413081.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.3561.480.611.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2FPE1.4553.88340262206681.1470.160.15650.21525.32
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]
-0.9691.907-0.939
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.681
r_dihedral_angle_4_deg19.746
r_dihedral_angle_3_deg15.704
r_dihedral_angle_1_deg8.553
r_lrange_it6.956
r_scangle_it6.844
r_scangle_other6.842
r_lrange_other6.828
r_scbond_it5.808
r_scbond_other5.807
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.681
r_dihedral_angle_4_deg19.746
r_dihedral_angle_3_deg15.704
r_dihedral_angle_1_deg8.553
r_lrange_it6.956
r_scangle_it6.844
r_scangle_other6.842
r_lrange_other6.828
r_scbond_it5.808
r_scbond_other5.807
r_mcangle_other5.044
r_mcangle_it4.988
r_mcbond_it4.372
r_mcbond_other4.337
r_rigid_bond_restr3.393
r_angle_refined_deg1.689
r_angle_other_deg1.418
r_symmetry_xyhbond_nbd_refined0.288
r_symmetry_nbd_refined0.252
r_nbd_other0.235
r_nbd_refined0.232
r_symmetry_nbd_other0.203
r_xyhbond_nbd_refined0.199
r_nbtor_refined0.179
r_ncsr_local_group_40.126
r_ncsr_local_group_10.116
r_ncsr_local_group_60.11
r_ncsr_local_group_50.094
r_ncsr_local_group_30.088
r_chiral_restr0.086
r_ncsr_local_group_20.083
r_symmetry_nbtor_other0.081
r_symmetry_xyhbond_nbd_other0.079
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2069
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing