3GSQ | pdb_00003gsq

Crystal structure of the binary complex between HLA-A2 and HCMV NLV-M5S peptide variant

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	9-20% PEG 6000, 0.1M tri-Na Citrate, 0-0.1M NaCl, pH 6.5, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.047	α = 90
b = 80.897	β = 114.17
c = 57.659	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	ADSC QUANTUM 4		2008-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.12	50	93.4	0.042	0.042	27.71	3.6		27129			29.46

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.12	2.19	69.7		0.169	0.169	6.7	2.4	1656

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.12	14.92	27129	24142	2487	95.93	0.199	0.199	0.196	0.2	0.246	RANDOM	35.564

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]
-0.02		-0.06	0.01		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.144
r_dihedral_angle_4_deg	16.096
r_dihedral_angle_3_deg	15.583
r_dihedral_angle_1_deg	6.261
r_scangle_it	2.499
r_scbond_it	1.67
r_angle_refined_deg	1.232
r_mcangle_it	1.165
r_mcbond_it	0.692
r_nbtor_refined	0.293

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.144
r_dihedral_angle_4_deg	16.096
r_dihedral_angle_3_deg	15.583
r_dihedral_angle_1_deg	6.261
r_scangle_it	2.499
r_scbond_it	1.67
r_angle_refined_deg	1.232
r_mcangle_it	1.165
r_mcbond_it	0.692
r_nbtor_refined	0.293
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.134
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3202
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	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.