4PG9

MHC Class I in complex with Sendai virus nucleoprotein peptide FAPGNYPAL

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	sodium/potassium phosphate buffer 1.9M, MPD 1%, glycerol (cryoprotection)

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.721	α = 90
b = 136.533	β = 90
c = 45.203	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	MARMOSAIC 225 mm CCD		2012-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	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	2.4	40	98.3	0.127	0.127	8.3	3.8	21454	21454			20.79

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)
	2.4	2.53	98.9		0.488	0.488	2.6	3.8

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	3P9L	2.4	40	21436	1101	97.5	0.2124	0.2104	0.2499	RANDOM	26.523

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]
-1.16			0.56		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.404
r_dihedral_angle_4_deg	14.439
r_dihedral_angle_3_deg	12.453
r_dihedral_angle_1_deg	5.747
r_mcangle_it	1.303
r_angle_refined_deg	1.01
r_mcbond_it	0.747
r_mcbond_other	0.747
r_angle_other_deg	0.682
r_chiral_restr	0.063
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3136
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	60

Software

Software
Software Name	Purpose
SCALA	data scaling
XDS	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
REFMAC	refinement