2GTZ | pdb_00002gtz

Human Class I MHC HLA-A2 in complex with the nonameric Melan-A/MART-1(27-35) peptide having A28L substitution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TVB	PDB entry 1TVB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	PEG 3350 24%, MES 0.025M, NH4Cl 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.4	α = 90
b = 84.31	β = 90.13
c = 84.14	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	MARMOSAIC 300 mm CCD		2005-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.979	APS	23-ID-D

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	1.7	20	97	0.1	13.1	3.5	90210	87504		1	16.7

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	1.7	1.76	85.6		0.479	2.1	2.6	7671

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 (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	PDB entry 1TVB	1.7	20	1	90185	83098	4382	96.95	0.17412	0.17412	0.17184	0.17	0.2173	0.22	RANDOM	21.719

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]
-0.69		0.17	1.6		-0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.731
r_dihedral_angle_4_deg	20.887
r_dihedral_angle_3_deg	14.818
r_dihedral_angle_1_deg	6.135
r_scangle_it	4.624
r_scbond_it	2.882
r_angle_refined_deg	1.71
r_mcangle_it	1.701
r_mcbond_it	0.939
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.731
r_dihedral_angle_4_deg	20.887
r_dihedral_angle_3_deg	14.818
r_dihedral_angle_1_deg	6.135
r_scangle_it	4.624
r_scbond_it	2.882
r_angle_refined_deg	1.71
r_mcangle_it	1.701
r_mcbond_it	0.939
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.199
r_metal_ion_refined	0.192
r_xyhbond_nbd_refined	0.189
r_nbd_refined	0.162
r_chiral_restr	0.154
r_symmetry_vdw_refined	0.124
r_bond_refined_d	0.016
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6288
Nucleic Acid Atoms
Solvent Atoms	812
Heterogen Atoms	38

Software

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

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.