Experiment: 8W86

HLA-DQ2.5-B/C hordein peptide in complex with DQN0385AE02

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VG1	7VG1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	294	0.1 M MES monohydrate (pH5.5), 12.0 %w/v Polyethylene glycol 8,000, 0.1 M Calcium acetate hydrate, and 30 %v/v Ethylene glycol as cryoprotectant

Crystal Properties
Matthews coefficient	Solvent content
3.12	60.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.701	α = 90
b = 127.187	β = 104.45
c = 130.365	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		2019-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00000	SPring-8	BL45XU

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	2.236	126.22	93.6	0.1016	0.1127	0.048	0.998	10.72	5.32		77604

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)
	2.236	2.457	61.4		1.2292	1.344	0.5384	0.511	1.56	5.99	3880

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	7VG1	2.236	126.22	77604	4001	69.1	0.243	0.241	0.2338	0.2804	0.2763	RANDOM	54.72

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]
0.3778		-0.0732	-0.4886		0.1108

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	18.31
t_omega_torsion	3.33
t_angle_deg	1.03
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10808
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	28

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
autoPROC	data processing
PHASER	phasing