2Q1M | pdb_00002q1m

Crystal Structure of human GITRL

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	25% PEG 3350, 0.1 M Sodium Acetate pH 4.5, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.691	α = 90
b = 72.691	β = 90
c = 53.101	γ = 120

Symmetry
Space Group	P 63

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 4		2006-04-08	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 315		2006-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.9795	NSLS	X4A
2	SYNCHROTRON	NSLS BEAMLINE X29A	1.009	NSLS	X29A

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	2.3	21.7	99.9	0.071	10.5	10.8	7131	7131

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	100			10.8	693

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	2.3	21.7	7117	7117	331	99.41	0.217	0.217	0.215	0.2086	0.257	0.2433	RANDOM	44.57

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]
0.64	0.32		0.64		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.981
r_dihedral_angle_4_deg	18.478
r_dihedral_angle_3_deg	17.099
r_dihedral_angle_1_deg	7.327
r_scangle_it	2.444
r_scbond_it	1.635
r_mcangle_it	1.539
r_angle_refined_deg	1.431
r_mcbond_it	0.899
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.249
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	947
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building