2ZOL | pdb_00002zol

Crystal structure of H-2Db in complex with the W513S variant of JHMV epitope S510

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BZ9	PDB ENTRY 1BZ9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	294	0.1M sodium citrate, 28% PEG 3350, 0.15M lithium sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.561	α = 90
b = 71.033	β = 103.45
c = 86.999	γ = 90

Symmetry
Space Group	P 1 2 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	MAR CCD 165 mm		2007-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.999	Australian Synchrotron	MX1

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	2.7	54.39	99.3	0.083	0.083	8.2	3	27219	27219			51.6

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)
	2.7	2.85	99.1		0.33	0.33	3.2	3	3940

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BZ9	2.7	33.7	25849	25849	1368	99.04	0.2564	0.2564	0.2537	0.2477	0.30726	0.297	RANDOM	26.996

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		0.21	0.04		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.546
r_dihedral_angle_3_deg	17.33
r_dihedral_angle_4_deg	15.472
r_dihedral_angle_1_deg	5.114
r_scangle_it	1.061
r_angle_refined_deg	0.96
r_mcangle_it	0.954
r_scbond_it	0.663
r_mcbond_it	0.529
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.19
r_nbd_refined	0.174
r_symmetry_hbond_refined	0.134
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.066
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5991
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing