7NYN

Mutant Y526A of SH3 domain of JNK-interacting Protein 1 (JIP1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7NYK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	0.1 M HEPES pH 7.5, 1-5 % PEG 400, 2-2.5 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.2	61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 210.639	α = 90
b = 62.485	β = 90
c = 87.056	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2020-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.96546	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.537	49.35	99.8	0.99	11.9	6.3		329963

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.63	98.7		0.31

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7NYK	1.537	49.35	171114	1798	99.932	0.138	0.1378	0.1796	37.594

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]
-1.416			3.466		-2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.582
r_dihedral_angle_4_deg	15.775
r_dihedral_angle_3_deg	15.729
r_scangle_it	10.672
r_scangle_other	10.671
r_scbond_it	9.23
r_scbond_other	9.229
r_dihedral_angle_1_deg	8.95
r_lrange_it	8.475
r_lrange_other	8.474
r_mcangle_other	5.896
r_mcangle_it	5.894
r_rigid_bond_restr	5.518
r_mcbond_it	5.318
r_mcbond_other	5.268
r_angle_refined_deg	1.864
r_angle_other_deg	1.415
r_symmetry_nbd_refined	0.246
r_nbd_other	0.226
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.21
r_symmetry_nbd_other	0.2
r_nbtor_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.151
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.036
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6057
Nucleic Acid Atoms
Solvent Atoms	700
Heterogen Atoms	280

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing