6SS9 | pdb_00006ss9

Human Leukocyte Antigen Class I A02 Carrying LLWNGPMHV

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5N6B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1 M Sodium Cacodylate pH 6.5, 0.2 M Ammonium Sulphate, 20 % PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 199.751	α = 90
b = 48.261	β = 123.47
c = 117.754	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 PILATUS3 S 6M		2017-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2.52	29.43	98.6	0.077	0.091	0.047	0.996	9.6	3.6		31568

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	2.52	2.59	89.6		0.686	0.798	0.403	0.784		3.7

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	5N6B	2.7	29.43	24732	1287	99.15	0.2362	0.2327	0.2385	0.301	0.2983	RANDOM	69.064

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]
4.58		2.86	-3.42		-2.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.292
r_dihedral_angle_4_deg	21.779
r_dihedral_angle_3_deg	20.385
r_dihedral_angle_1_deg	8.786
r_angle_refined_deg	1.691
r_angle_other_deg	0.885
r_chiral_restr	0.071
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6332
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	59

Software

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