2GTW | pdb_00002gtw

Human Class I MHC HLA-A2 in complex with the nonameric Melan-A/MART-1(27-35) peptide having A27L 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, HCOOK 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.309	α = 90
b = 84.271	β = 90.11
c = 84.293	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		2005-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	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	1.548	20	93.2	0.108	14.8	3.1	118490	110421	1	1	17

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	1.548	1.61	71.2		0.354	2.11	1.5	8400

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	1.548	20	1	118485	104852	5541	93.17	0.18317	0.18317	0.18135	0.18	0.21768	0.22	RANDOM	22.072

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]
-0.84		0.39	1.08		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.491
r_dihedral_angle_4_deg	19.177
r_dihedral_angle_3_deg	15.348
r_dihedral_angle_1_deg	6.205
r_scangle_it	4.882
r_scbond_it	3.035
r_mcangle_it	1.884
r_angle_refined_deg	1.73
r_mcbond_it	1.065
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.491
r_dihedral_angle_4_deg	19.177
r_dihedral_angle_3_deg	15.348
r_dihedral_angle_1_deg	6.205
r_scangle_it	4.882
r_scbond_it	3.035
r_mcangle_it	1.884
r_angle_refined_deg	1.73
r_mcbond_it	1.065
r_nbtor_refined	0.311
r_symmetry_hbond_refined	0.212
r_xyhbond_nbd_refined	0.184
r_nbd_refined	0.164
r_chiral_restr	0.158
r_symmetry_vdw_refined	0.139
r_metal_ion_refined	0.081
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	672
Heterogen Atoms	44

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.