1KPU

High resolution crystal structure of the MHC class I complex H-2Kb/VSV8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VAA	PDB entry 2vaa, chains A and B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	K/NA PHOSPHATE, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.086	α = 90
b = 88.121	β = 90
c = 45.24	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	CUSTOM-MADE		2001-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.033	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.5	42	92.5	0.113	9.8	6.3		81282		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	71.5		0.431	2.9	3.7	6180

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2vaa, chains A and B	1.5	41.89	74678	3977	96.85	0.18552	0.18432	0.20814	RANDOM	17.187

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]
-0.41			0.55		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.108
r_scangle_it	4.609
r_dihedral_angle_1_deg	4.602
r_angle_other_deg	3.173
r_scbond_it	2.755
r_mcangle_it	1.902
r_angle_refined_deg	1.643
r_mcbond_it	1.008
r_nbtor_other	0.434
r_symmetry_vdw_other	0.299
r_symmetry_vdw_refined	0.234
r_nbd_refined	0.216
r_xyhbond_nbd_other	0.204
r_nbd_other	0.201
r_chiral_restr	0.169
r_xyhbond_nbd_refined	0.165
r_symmetry_hbond_refined	0.12
r_bond_refined_d	0.014
r_gen_planes_other	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3121
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing