5NQ2 | pdb_00005nq2

'Porcine (Sus scrofa) Major Histocompatibility Complex, class I, presenting IAYERMCNI

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	JBS Screen, condition F10: 10% Jeffamine M-600, 0.1 M Na Citrate, pH 5.6, 10 mM Ferric(III)Cl

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.478	α = 90
b = 80.843	β = 119.66
c = 61.964	γ = 90

Symmetry
Space Group	C 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	PIXEL	DECTRIS PILATUS 6M		2016-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.54	57.3	97.6	0.057	0.067	0.034	0.998	12.7	3.8		57504			19.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.62	97.2		0.66	0.764	0.38	0.778		3.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PHASER	1.54	57.3	54582	2921	97.38	0.1945	0.1914	0.2001	0.2514	0.258	RANDOM	22.756

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]
1.03		-0.81	1.78		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.246
r_dihedral_angle_4_deg	15.213
r_sphericity_free	14.014
r_dihedral_angle_3_deg	12.996
r_sphericity_bonded	5.354
r_dihedral_angle_1_deg	5.102
r_rigid_bond_restr	3.331
r_angle_refined_deg	1.951
r_angle_other_deg	1.071
r_chiral_restr	0.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.246
r_dihedral_angle_4_deg	15.213
r_sphericity_free	14.014
r_dihedral_angle_3_deg	12.996
r_sphericity_bonded	5.354
r_dihedral_angle_1_deg	5.102
r_rigid_bond_restr	3.331
r_angle_refined_deg	1.951
r_angle_other_deg	1.071
r_chiral_restr	0.056
r_bond_refined_d	0.019
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3151
Nucleic Acid Atoms
Solvent Atoms	434
Heterogen Atoms	5

Software

Software
Software Name	Purpose
Aimless	data scaling
xia2	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
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 R01GM157729.