1TVH | pdb_00001tvh

Crystal structure of Modified Melanoma Antigen gp100(209-T2M) Bound to Human Class I MHC HLA-A2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BOR	PDB Entry 1BOR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	PEG 3350, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.407	α = 90
b = 84.485	β = 90.11
c = 84.014	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	CUSTOM-MADE		2004-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.98731	APS	19-BM

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	1.8	20	98.7	0.065	16.3	2.8	75145	74168		1	17.58

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	1.8	1.86	97		0.4	2.72	2.6	7284

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB Entry 1BOR	1.802	10	2	74883	70064	3703	98.51	0.18795	0.18489	0.19	0.24651	0.25	RANDOM	14.467

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]
-0.9		-0.76	1.2		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.629
r_scangle_it	5.29
r_scbond_it	3.528
r_angle_refined_deg	2.14
r_mcangle_it	2.008
r_mcbond_it	1.211
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.182
r_symmetry_hbond_refined	0.182
r_nbd_refined	0.168

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.629
r_scangle_it	5.29
r_scbond_it	3.528
r_angle_refined_deg	2.14
r_mcangle_it	2.008
r_mcbond_it	1.211
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.182
r_symmetry_hbond_refined	0.182
r_nbd_refined	0.168
r_symmetry_vdw_refined	0.117
r_bond_refined_d	0.022
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6312
Nucleic Acid Atoms
Solvent Atoms	726
Heterogen Atoms	168

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction

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.