1S7Q | pdb_00001s7q

Crystal structures of the murine class I major histocompatibility complex H-2Kb in complex with LCMV-derived gp33 index peptide and three of its escape variants

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1N59	PDB entry 1N59

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	sodium/potassium phosphate, Methyl pentane diol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.09	59.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.22	α = 90
b = 135.871	β = 90
c = 45.168	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARRESEARCH		2003-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I711	0.97	MAX II	I711

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.99	141.42	98.9			38269	37848		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.99	2.1	94

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 (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 1N59	1.99	37.53	38269	35920	1894	98.79	0.18281	0.18142	0.21	0.20933	0.23	RANDOM	18.251

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]
0.04			0.18		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.621
r_scangle_it	4.228
r_scbond_it	2.544
r_mcangle_it	1.605
r_angle_refined_deg	1.488
r_angle_other_deg	0.889
r_mcbond_it	0.821
r_nbd_other	0.255
r_symmetry_vdw_other	0.227
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.183
r_symmetry_vdw_refined	0.174
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.11
r_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3130
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing