6Z9W | pdb_00006z9w

Human Class I Major Histocompatibility Complex, A02 allele, presenting LLGWVFAQV

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	295	PACT premier screen, condition D02: 0.1M MMT buffer, 25% PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.725	α = 90
b = 69.208	β = 90
c = 88.617	γ = 90

Symmetry
Space Group	P 1 21 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		2017-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97622	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	2.7	29.94	99.8	0.212	0.23	0.088	0.991	7.8	6.9		19779

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	2.7	2.77	99.9		1.392	1.496	0.543	0.625		7.5

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	5EUL	2.7	29.94	18791	971	98.54	0.2036	0.1997	0.2038	0.2806	0.2818	RANDOM	42.764

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]
12.65		-4.05	-1.89		-10.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.789
r_dihedral_angle_4_deg	22.732
r_dihedral_angle_3_deg	22.119
r_dihedral_angle_1_deg	9.896
r_angle_refined_deg	1.537
r_angle_other_deg	1.194
r_chiral_restr	0.064
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6316
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms

Software

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