7NYL

Mutant H493A 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, 2-2.5 M Ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
1.936.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.055α = 90
b = 45.551β = 104.274
c = 46.006γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.9763ESRFID23-1

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
11.9345.5596.30.996.98.484431
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)
11.932.0377.90.661.18

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-VALUE7NYK1.9544.586831140399.8440.2070.20490.254531.846
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]
4.371-3.49-1.512-0.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.694
r_dihedral_angle_4_deg20.172
r_dihedral_angle_3_deg19.221
r_dihedral_angle_1_deg10.264
r_lrange_it8.133
r_lrange_other8.13
r_scangle_it6.104
r_scangle_other6.1
r_scbond_it3.822
r_scbond_other3.818
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.694
r_dihedral_angle_4_deg20.172
r_dihedral_angle_3_deg19.221
r_dihedral_angle_1_deg10.264
r_lrange_it8.133
r_lrange_other8.13
r_scangle_it6.104
r_scangle_other6.1
r_scbond_it3.822
r_scbond_other3.818
r_mcangle_it3.785
r_mcangle_other3.782
r_mcbond_other2.483
r_mcbond_it2.481
r_angle_refined_deg1.673
r_angle_other_deg1.233
r_symmetry_xyhbond_nbd_refined0.307
r_symmetry_nbd_refined0.204
r_symmetry_nbd_other0.199
r_xyhbond_nbd_refined0.186
r_nbd_refined0.184
r_nbd_other0.179
r_nbtor_refined0.176
r_ncsr_local_group_10.14
r_symmetry_nbtor_other0.08
r_chiral_restr0.064
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1003
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing