7NYK

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	2FPE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293.15	0.1 M HEPES pH 7.5; 1-5 PEG 400; 2-2.5 M Ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.3	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.399	α = 90
b = 82.128	β = 90
c = 46.849	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		2020-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.96546	ESRF	ID30B

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	1.35	53.883	91.8	0.993	9.5	4.6		41308		1.5

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	1.356	1.48			0.61	1.5

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	2FPE	1.45	53.883	40262	2066	81.147	0.16	0.1565	0.215	25.32

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]
-0.969			1.907		-0.939

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.681
r_dihedral_angle_4_deg	19.746
r_dihedral_angle_3_deg	15.704
r_dihedral_angle_1_deg	8.553
r_lrange_it	6.956
r_scangle_it	6.844
r_scangle_other	6.842
r_lrange_other	6.828
r_scbond_it	5.808
r_scbond_other	5.807
r_mcangle_other	5.044
r_mcangle_it	4.988
r_mcbond_it	4.372
r_mcbond_other	4.337
r_rigid_bond_restr	3.393
r_angle_refined_deg	1.689
r_angle_other_deg	1.418
r_symmetry_xyhbond_nbd_refined	0.288
r_symmetry_nbd_refined	0.252
r_nbd_other	0.235
r_nbd_refined	0.232
r_symmetry_nbd_other	0.203
r_xyhbond_nbd_refined	0.199
r_nbtor_refined	0.179
r_ncsr_local_group_4	0.126
r_ncsr_local_group_1	0.116
r_ncsr_local_group_6	0.11
r_ncsr_local_group_5	0.094
r_ncsr_local_group_3	0.088
r_chiral_restr	0.086
r_ncsr_local_group_2	0.083
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.079
r_bond_refined_d	0.013
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	2069
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms

Software

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