7NYM

Mutant V517A - 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
2.3	47

Crystal Data

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

Symmetry
Space Group	P 21 21 21

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		2020-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

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	1.45	63.976	94	0.99	7	12.5		45428

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	1.454	1.518			0.46	1.3

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	1.614	63.976	36326	1815	99.967	0.135	0.1314	0.1976	21.598

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]
-0.658			1.586		-0.928

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.76
r_dihedral_angle_3_deg	15.267
r_dihedral_angle_4_deg	14.482
r_dihedral_angle_1_deg	9.433
r_scangle_it	6.761
r_scangle_other	6.761
r_lrange_other	5.653
r_lrange_it	5.652
r_scbond_other	5.538
r_scbond_it	5.535
r_mcangle_it	2.922
r_mcangle_other	2.921
r_rigid_bond_restr	2.844
r_mcbond_it	2.381
r_mcbond_other	2.378
r_angle_refined_deg	1.68
r_angle_other_deg	1.373
r_nbd_refined	0.318
r_nbd_other	0.25
r_symmetry_nbd_other	0.227
r_symmetry_xyhbond_nbd_refined	0.2
r_xyhbond_nbd_refined	0.177
r_symmetry_nbd_refined	0.173
r_nbtor_refined	0.169
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2020
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing