8S85 | pdb_00008s85

Crystal structure of JAK1 JH1 domain in complex with an inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	0.1 M MES pH 5-6 and 25-35% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.41	49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.038	α = 90
b = 174.03	β = 94.5
c = 44.893	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	CCD	ADSC QUANTUM 315r		2011-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.979500	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	1.75	87.01	96.2	0.05	0.059	17.8	3.5		60553

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.82			0.547	0.657

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.75	87.01	60553	2941	96.35	0.20988	0.20791	0.2162	0.2496	0.2569	RANDOM	35.589

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]
-0.93		0.31	-0.56		1.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.925
r_dihedral_angle_4_deg	18.534
r_dihedral_angle_3_deg	12.29
r_dihedral_angle_1_deg	6.083
r_scangle_it	5.581
r_scbond_it	4.035
r_mcangle_it	2.847
r_mcbond_it	1.929
r_angle_refined_deg	1.33
r_angle_other_deg	1.285
r_mcbond_other	0.484
r_symmetry_vdw_refined	0.245
r_symmetry_vdw_other	0.207
r_nbd_refined	0.186
r_nbd_other	0.167
r_nbtor_refined	0.165
r_symmetry_hbond_refined	0.133
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.076
r_nbtor_other	0.069
r_symmetry_metal_ion_refined	0.036
r_metal_ion_refined	0.017
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4682
Nucleic Acid Atoms
Solvent Atoms	438
Heterogen Atoms	43

Software

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