7NYO

Mutant A541L of 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 and 2-2.5 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
240.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.093α = 90
b = 67.104β = 126.701
c = 59.142γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873128ESRFID23-2

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
11.447.41891.90.9825.55.341884
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)
11.41.510.741.5

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-VALUE7NYK1.447.41841728211670.4120.1970.19230.275923.522
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]
1.5920.556-0.402-0.956
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.678
r_dihedral_angle_3_deg17.035
r_dihedral_angle_4_deg15.366
r_dihedral_angle_1_deg8.5
r_lrange_it7.576
r_lrange_other6.805
r_scangle_it4.787
r_scangle_other4.785
r_mcangle_it3.907
r_mcangle_other3.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.678
r_dihedral_angle_3_deg17.035
r_dihedral_angle_4_deg15.366
r_dihedral_angle_1_deg8.5
r_lrange_it7.576
r_lrange_other6.805
r_scangle_it4.787
r_scangle_other4.785
r_mcangle_it3.907
r_mcangle_other3.905
r_scbond_it3.886
r_scbond_other3.884
r_mcbond_it3.231
r_mcbond_other3.23
r_rigid_bond_restr3.212
r_angle_refined_deg1.665
r_angle_other_deg1.315
r_nbd_refined0.278
r_xyhbond_nbd_refined0.266
r_symmetry_xyhbond_nbd_refined0.251
r_symmetry_nbd_refined0.231
r_nbd_other0.228
r_symmetry_nbd_other0.221
r_nbtor_refined0.174
r_symmetry_xyhbond_nbd_other0.135
r_chiral_restr0.084
r_symmetry_nbtor_other0.079
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.005
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2013
Nucleic Acid Atoms
Solvent Atoms525
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing