6QZD

HLA-DR1 with SGP Influenza Matrix Peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DLH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	291	0.1 M Tris 0.2 M NH4 SO4 25% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.42	α = 90
b = 76.73	β = 93.5
c = 90.13	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 PILATUS3 S 6M		2016-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97626	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.66	55.54	99.1	0.196	0.229	0.116	6.3	3.7		26304

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	2.66	2.73	98.7		1.043	1.215	0.616	0.466	1.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1DLH	2.66	55.537	26290	1267	98.95	0.203	0.2001	0.2539	42.325

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]
-2.441		0.044	-0.072		2.489

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.351
r_dihedral_angle_4_deg	21.793
r_dihedral_angle_3_deg	20.234
r_dihedral_angle_1_deg	7.858
r_lrange_it	4.913
r_scangle_it	2.228
r_mcangle_it	1.989
r_angle_refined_deg	1.684
r_scbond_it	1.373
r_mcbond_it	1.134
r_nbtor_refined	0.317
r_symmetry_nbd_refined	0.245
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.176
r_ncsr_local_group_3	0.164
r_symmetry_xyhbond_nbd_refined	0.142
r_chiral_restr	0.127
r_ncsr_local_group_1	0.098
r_ncsr_local_group_2	0.092
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6262
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	49

Software

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