2ZOK

Crystal structure of H-2Db in complex with JHMV epitope S510

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	294	0.1M sodium citrate, 28% PEG 3350, 0.2M lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.538	α = 90
b = 86.056	β = 90.01
c = 152.072	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 210		2006-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	1.0	APS	14-BM-C

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	2.1	58.4	95.4	0.056	0.056	8.2	2.8	113937	113937			30.4

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	2.1	2.21	97.3		0.185	0.185	4.8	2.7	16934

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1BZ9	2.1	56.98	108198	108198	5737	95.05	0.20936	0.20936	0.20635	0.26614	RANDOM	27.903

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]
1.2		0.13	-1.07		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.857
r_dihedral_angle_4_deg	17.511
r_dihedral_angle_3_deg	16.038
r_dihedral_angle_1_deg	7.175
r_scangle_it	5.21
r_scbond_it	3.672
r_mcangle_it	2.66
r_mcbond_it	1.791
r_angle_refined_deg	1.741
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.857
r_dihedral_angle_4_deg	17.511
r_dihedral_angle_3_deg	16.038
r_dihedral_angle_1_deg	7.175
r_scangle_it	5.21
r_scbond_it	3.672
r_mcangle_it	2.66
r_mcbond_it	1.791
r_angle_refined_deg	1.741
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.236
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.158
r_chiral_restr	0.124
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12061
Nucleic Acid Atoms
Solvent Atoms	969
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

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 R01GM133198.