7CML

The Crystal Structure of human JNK2 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NPC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Na/K PO4, 20% PEG3,350

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.004	α = 90
b = 102.004	β = 90
c = 70.088	γ = 90

Symmetry
Space Group	P 4

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 PILATUS3 6M		2020-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.97915	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.15	19.616	99.8	0.141	10.8	9.1		39267

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.22			1.269

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	3npc	2.15	19.616	39264	1929	99.794	0.286	0.2842	0.3274	36.292

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]
0.703			0.703		-1.406

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.273
r_dihedral_angle_4_deg	17.112
r_dihedral_angle_3_deg	16.065
r_dihedral_angle_1_deg	6.748
r_lrange_it	5.027
r_lrange_other	5.024
r_mcangle_it	2.982
r_mcangle_other	2.981
r_scangle_it	2.928
r_scangle_other	2.927
r_mcbond_it	1.747
r_mcbond_other	1.746
r_scbond_it	1.693
r_scbond_other	1.692
r_angle_refined_deg	1.227
r_angle_other_deg	1.112
r_nbd_refined	0.189
r_nbd_other	0.181
r_symmetry_nbd_other	0.173
r_symmetry_nbd_refined	0.173
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.053
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5406
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms

Software

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