5NQ1 | pdb_00005nq1

Porcine (Sus scrofa) Major Histocompatibility Complex, class I, with human beta2 micro globulin, presenting DFEREGYSL

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QQ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	PACT screen, condition D02: 0.1M MMT Buffer, pH 5.0, 25% PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.388	α = 81.24
b = 60.288	β = 67.59
c = 65.645	γ = 67.94

Symmetry
Space Group	P 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 PILATUS3 6M		2016-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

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	2.14	55.87	96.9	0.128	0.172	0.115	0.979	3.4	1.9		41686

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	2.14	2.2	96		0.669	0.91	0.614	0.522		1.9	3024

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	3QQ3	2.14	55.87	39657	2021	96.88	0.2226	0.2195	0.22	0.283	0.29	RANDOM	28.043

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]
-1.74	-0.23	-0.32	0.01	0.29	0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.258
r_dihedral_angle_4_deg	21.301
r_dihedral_angle_3_deg	18.145
r_dihedral_angle_1_deg	7.289
r_angle_refined_deg	1.931
r_angle_other_deg	1.115
r_chiral_restr	0.125
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.258
r_dihedral_angle_4_deg	21.301
r_dihedral_angle_3_deg	18.145
r_dihedral_angle_1_deg	7.289
r_angle_refined_deg	1.931
r_angle_other_deg	1.115
r_chiral_restr	0.125
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6294
Nucleic Acid Atoms
Solvent Atoms	356
Heterogen Atoms	28

Software

Software
Software Name	Purpose
Aimless	data scaling
DIALS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
xia2	data reduction

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.