2APW | pdb_00002apw

Crystal Structure of the G17E/A52V/S54N/K66E/E80V/L81S/T87S/G96V variant of the murine T cell receptor V beta 8.2 domain

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	2.0 M Sodium Malonate, 0.2 % dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.521	α = 90
b = 74.552	β = 90
c = 113.045	γ = 90

Symmetry
Space Group	I 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	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2003-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.64	33.6	98.3			17349	17060	2	4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.78	42

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	MOLECULAR REPLACEMENT	THROUGHOUT	2	30	9697	9613	465	99.13	0.199	0.198	0.197	0.59	0.239	0.62	RANDOM	16.463

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]
-0.91			0.85		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.703
r_dihedral_angle_4_deg	22.312
r_dihedral_angle_3_deg	14.275
r_dihedral_angle_1_deg	6.646
r_scangle_it	4.145
r_scbond_it	3.12
r_angle_refined_deg	1.639
r_mcangle_it	1.586
r_mcbond_it	1.069
r_symmetry_hbond_refined	0.396

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.703
r_dihedral_angle_4_deg	22.312
r_dihedral_angle_3_deg	14.275
r_dihedral_angle_1_deg	6.646
r_scangle_it	4.145
r_scbond_it	3.12
r_angle_refined_deg	1.639
r_mcangle_it	1.586
r_mcbond_it	1.069
r_symmetry_hbond_refined	0.396
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.29
r_nbd_refined	0.285
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.121
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	832
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	7

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.