7NYM

Mutant V517A - SH3 domain of JNK-interacting Protein 1 (JIP1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NYK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52930.1 M HEPES pH 7.5, 1-5 % PEG 400, 2-2.5 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.12α = 90
b = 84.254β = 90
c = 98.315γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8731ESRFID23-2

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
11.4563.976940.99712.545428
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)
11.4541.5180.461.3

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-VALUE7NYK1.61463.97636326181599.9670.1350.13140.197621.598
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]
-0.6581.586-0.928
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.76
r_dihedral_angle_3_deg15.267
r_dihedral_angle_4_deg14.482
r_dihedral_angle_1_deg9.433
r_scangle_it6.761
r_scangle_other6.761
r_lrange_other5.653
r_lrange_it5.652
r_scbond_other5.538
r_scbond_it5.535
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.76
r_dihedral_angle_3_deg15.267
r_dihedral_angle_4_deg14.482
r_dihedral_angle_1_deg9.433
r_scangle_it6.761
r_scangle_other6.761
r_lrange_other5.653
r_lrange_it5.652
r_scbond_other5.538
r_scbond_it5.535
r_mcangle_it2.922
r_mcangle_other2.921
r_rigid_bond_restr2.844
r_mcbond_it2.381
r_mcbond_other2.378
r_angle_refined_deg1.68
r_angle_other_deg1.373
r_nbd_refined0.318
r_nbd_other0.25
r_symmetry_nbd_other0.227
r_symmetry_xyhbond_nbd_refined0.2
r_xyhbond_nbd_refined0.177
r_symmetry_nbd_refined0.173
r_nbtor_refined0.169
r_chiral_restr0.09
r_symmetry_nbtor_other0.086
r_bond_refined_d0.011
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 Atoms2020
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing