3CVH

How TCR-like antibody recognizes MHC-bound peptide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CVI	PDB ENTRIES 3CVI AND 2VAA
experimental model	PDB	2VAA	PDB ENTRIES 3CVI AND 2VAA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6	293	0.2 M (NH4)2SO4, 0.1 M NaOAc, pH 4.6 containing 25% w/v polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.57	α = 90
b = 111.345	β = 90
c = 219.087	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	CCD	ADSC QUANTUM 4		2005-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A		NSLS	X4A

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	2.8	50	97.6				48272

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	95		0.429

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 3CVI AND 2VAA	2.9	19.98	41343	2203	100	0.223	0.219	0.296	RANDOM	42.85

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]
-0.4			-0.32		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.455
r_dihedral_angle_3_deg	18.148
r_dihedral_angle_4_deg	17.365
r_dihedral_angle_1_deg	5.569
r_scangle_it	1.326
r_angle_refined_deg	1.089
r_scbond_it	0.77
r_mcangle_it	0.617
r_mcbond_it	0.353
r_nbtor_refined	0.303
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.187
r_xyhbond_nbd_refined	0.149
r_symmetry_hbond_refined	0.147
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12710
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms

Software

Software
Software Name	Purpose
PHASER	phasing
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction