1XR9 | pdb_00001xr9

Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A1M	B*1501/LEKARGSTY Complex without Peptide

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	277	0.2M NH4Ac, 0.1M tri-Sodium Citrate dihydrate, pH 5.6, 30% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.359	α = 90
b = 81.389	β = 90
c = 109.969	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	IMAGE PLATE	MAR scanner 345 mm plate		2004-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.84140	EMBL/DESY, HAMBURG	BW7B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.776	31.654	97.44	0.068	14.2	3.7		43204		-3	17.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.87	83.32		0.298	2.5	3.7	19646

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FOURIER SYNTHESIS	THROUGHOUT	B*1501/LEKARGSTY Complex without Peptide	1.788	19.083	43303	41032	2172	94.756	0.18	0.17968	0.17695	0.19	0.23151	0.24	RANDOM	20.306

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.732
r_dihedral_angle_4_deg	17.408
r_dihedral_angle_3_deg	13.855
r_dihedral_angle_1_deg	6.004
r_scangle_it	3.749
r_scbond_it	2.354
r_mcangle_it	1.498
r_angle_refined_deg	1.437
r_mcbond_it	0.973
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.732
r_dihedral_angle_4_deg	17.408
r_dihedral_angle_3_deg	13.855
r_dihedral_angle_1_deg	6.004
r_scangle_it	3.749
r_scbond_it	2.354
r_mcangle_it	1.498
r_angle_refined_deg	1.437
r_mcbond_it	0.973
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.218
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.15
r_symmetry_hbond_refined	0.141
r_chiral_restr	0.103
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3147
Nucleic Acid Atoms
Solvent Atoms	595
Heterogen Atoms	20

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
CCP4	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.