7NYL

Mutant H493A of SH3 domain of JNK-interacting Protein 1 (JIP1)

X-RAY DIFFRACTION

---

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
1.9	36.1

Crystal Data

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

Symmetry
Space Group	P 1 21 1

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		2020-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9763	ESRF	ID23-1

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	1.93	45.55	96.3	0.99	6.9	8.4		8443		1

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	1.93	2.03	77.9		0.66	1.18

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	1.95	44.586	8311	403	99.844	0.207	0.2049	0.2545	31.846

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
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.694
r_dihedral_angle_4_deg	20.172
r_dihedral_angle_3_deg	19.221
r_dihedral_angle_1_deg	10.264
r_lrange_it	8.133
r_lrange_other	8.13
r_scangle_it	6.104
r_scangle_other	6.1
r_scbond_it	3.822
r_scbond_other	3.818
r_mcangle_it	3.785
r_mcangle_other	3.782
r_mcbond_other	2.483
r_mcbond_it	2.481
r_angle_refined_deg	1.673
r_angle_other_deg	1.233
r_symmetry_xyhbond_nbd_refined	0.307
r_symmetry_nbd_refined	0.204
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.186
r_nbd_refined	0.184
r_nbd_other	0.179
r_nbtor_refined	0.176
r_ncsr_local_group_1	0.14
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.064
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1003
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	36

Software

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