3GSR | pdb_00003gsr

Crystal structure of the binary complex between HLA-A2 and HCMV NLV-M5V 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	52.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.019	α = 90
b = 81.011	β = 114.56
c = 57.667	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 225 mm CCD		2008-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	1.95	50	96.4	0.065	0.65	15.35	3.8		36050			29.304

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)
	1.95	2.02	90.9		0.376	0.376	4.4	3.8	3011

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	1.95	14.91	36050	31902	3295	99.5	0.194	0.194	0.193	0.2	0.226	RANDOM	29.014

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	32.171
r_dihedral_angle_4_deg	18.696
r_dihedral_angle_3_deg	14.357
r_dihedral_angle_1_deg	5.562
r_scangle_it	2.313
r_scbond_it	1.546
r_mcangle_it	1.177
r_angle_refined_deg	1.171
r_mcbond_it	0.699
r_nbtor_refined	0.293

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.171
r_dihedral_angle_4_deg	18.696
r_dihedral_angle_3_deg	14.357
r_dihedral_angle_1_deg	5.562
r_scangle_it	2.313
r_scbond_it	1.546
r_mcangle_it	1.177
r_angle_refined_deg	1.171
r_mcbond_it	0.699
r_nbtor_refined	0.293
r_nbd_refined	0.188
r_symmetry_vdw_refined	0.144
r_symmetry_hbond_refined	0.131
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3198
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	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.