7Q6H | pdb_00007q6h

HUMAN JAK3 KINASE DOMAIN WITH 1-(4-((2-((1-methyl-1H-pyrazol-4-yl)amino)quinazolin-8-yl)amino)piperidin-1-yl)ethan-1-one

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		in house

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	8-20% PEG3350 and 0.2-0.3M ammonium sulphate (AS). 2% phenylurea

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.12	α = 90
b = 75.244	β = 90
c = 89.449	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 EIGER X 4M		2015-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.984	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.749	89.45	99.9	0.065	0.999	15.3	6.5		32901

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.87	99.9		0.605	0.848	2.6	6.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	in house	1.749	57.581	32841	1593	99.924	0.185	0.1827	0.19	0.2202	0.22	32.526

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]
1.246			-0.881		-0.365

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.896
r_dihedral_angle_4_deg	20.323
r_dihedral_angle_3_deg	13.621
r_lrange_it	6.605
r_lrange_other	6.604
r_dihedral_angle_1_deg	5.805
r_scangle_it	4.731
r_scangle_other	4.729
r_mcangle_it	3.205
r_mcangle_other	3.204
r_scbond_it	3.012
r_scbond_other	3.011
r_mcbond_it	2.151
r_mcbond_other	2.15
r_angle_other_deg	1.231
r_angle_refined_deg	1.161
r_nbd_refined	0.195
r_symmetry_nbd_other	0.176
r_nbd_other	0.173
r_symmetry_xyhbond_nbd_refined	0.166
r_symmetry_nbd_refined	0.163
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.161
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.058
r_chiral_restr	0.057
r_bond_refined_d	0.004
r_bond_other_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2259
Nucleic Acid Atoms
Solvent Atoms	373
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling