3MJ6 | pdb_00003mj6

Crystal structure of the gammadelta T cell costimulatory receptor Junctional Adhesion Molecule-Like Protein, JAML

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		OBTAINED BY MAD PHASING OF A TA6BR12 SOAKED JAML CRYSTAL AND SUBSEQUENT MR INTO THE NATIVE HIGH RESOLUTION DATA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.25	295	3.25 M NA-FORMATE, 0.1 M IMIDAZOLE, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.946	α = 90
b = 61.946	β = 90
c = 82.477	γ = 90

Symmetry
Space Group	P 43

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 210	KOHZU: DOUBLE CRYSTAL SI(111)	2005-02-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.07812, 0.99984	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.19	50	99.7	0.083	0.083	11.1	3.6		15924			34.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.19	2.24	99.2		0.415	0.415	2

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	OBTAINED BY MAD PHASING OF A TA6BR12 SOAKED JAML CRYSTAL AND SUBSEQUENT MR INTO THE NATIVE HIGH RESOLUTION DATA	2.19	50	15098	799	99.3	0.172	0.17	0.17	0.213	0.22	RANDOM	37.609

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]
0.16			0.16		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.55
r_dihedral_angle_4_deg	22.573
r_dihedral_angle_3_deg	16.657
r_dihedral_angle_1_deg	8.007
r_scangle_it	4.414
r_scbond_it	2.625
r_angle_refined_deg	1.716
r_mcangle_it	1.642
r_angle_other_deg	1.296
r_mcbond_it	0.862
r_symmetry_vdw_other	0.237
r_nbd_other	0.21
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.199
r_mcbond_other	0.183
r_nbtor_refined	0.17
r_symmetry_vdw_refined	0.141
r_chiral_restr	0.127
r_symmetry_hbond_refined	0.123
r_nbtor_other	0.096
r_metal_ion_refined	0.031
r_bond_refined_d	0.016
r_bond_other_d	0.01
r_gen_planes_refined	0.006
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1828
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	77

Software

Software
Software Name	Purpose
SHELX	model building
RESOLVE	model building
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
RESOLVE	phasing