6O9B | pdb_00006o9b

Crystal structure of HLA-A3*01 in complex with a wild-type beta-catenin peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XPG	PDB entry 2XPG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	292	0.1 M MES/imidazole, pH 6.5, 0.03 M diethylene glycol, 0.03 M triethylene glycol, 0.03 M tetraethylene glycol, 0.03 M pentaethylene glycol, 20% PEG500 MME, 10% PEG20000

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.77	α = 90
b = 152.77	β = 90
c = 84.835	γ = 120

Symmetry
Space Group	P 6 2 2

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 EIGER X 16M		2017-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.979	NSLS-II	17-ID-2

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	2.2	28.87	99.2	0.164	0.172	0.052	0.996	9.7	10.4		29999

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	2.2	2.26	91.2		1.081	1.138	0.348	0.704		9.8

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2XPG	2.2	28.87	28546	1452	99.17	0.1846	0.1824	0.2268	RANDOM	37.94

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]
0.27	0.13		0.27		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.352
r_dihedral_angle_4_deg	21.503
r_dihedral_angle_3_deg	16.423
r_dihedral_angle_1_deg	7.108
r_angle_refined_deg	1.932
r_angle_other_deg	1.536
r_chiral_restr	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.352
r_dihedral_angle_4_deg	21.503
r_dihedral_angle_3_deg	16.423
r_dihedral_angle_1_deg	7.108
r_angle_refined_deg	1.932
r_angle_other_deg	1.536
r_chiral_restr	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3159
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	138

Software

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

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.