5NQ0

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

X-RAY DIFFRACTION

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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 A09: 0.2 M LiCl, 0.1 M Sodium Acetate, pH 5.0, 20% PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.616	α = 104.36
b = 46.34	β = 101.21
c = 66.735	γ = 102.2

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		2017-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.1	39.28	92.3	0.086	0.998	6	1.9		170825

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.13	83.1		0.179	0.596	1.1	1.7

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	1.1	39.27	161372	8412	91.63	0.18999	0.18903	0.2	0.20852	0.22	RANDOM	17.308

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]
0.48	-0.25	-0.14	0.06	0.02	-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.145
r_dihedral_angle_4_deg	16.823
r_dihedral_angle_3_deg	13.646
r_long_range_B_refined	6.823
r_long_range_B_other	6.576
r_dihedral_angle_1_deg	6.211
r_angle_refined_deg	2.127
r_scangle_other	1.595
r_mcangle_it	1.076
r_mcangle_other	1.075
r_angle_other_deg	1.064
r_scbond_it	1.045
r_scbond_other	1.04
r_mcbond_it	0.645
r_mcbond_other	0.645
r_chiral_restr	0.118
r_bond_refined_d	0.019
r_gen_planes_refined	0.012
r_bond_other_d	0.007
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3117
Nucleic Acid Atoms
Solvent Atoms	538
Heterogen Atoms	82

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
xia2	data reduction
Aimless	data scaling
PHASER	phasing