5GSD

Crystal structure of LMP2 peptide from EBV in complex with HLA-A*11:01

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		290	0.2 M Ammonium acetate, 20% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.353	α = 90
b = 67.646	β = 90
c = 115.603	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2015-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.3	58.38	99.7	2.01	4.7		26775

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.3	58.38	18879	990	99.69	0.19854	0.19463	0.27314	RANDOM	31.596

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]
-1.55			0.87		0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.123
r_dihedral_angle_4_deg	19.341
r_dihedral_angle_3_deg	18.624
r_long_range_B_refined	8.293
r_long_range_B_other	8.29
r_dihedral_angle_1_deg	7.083
r_scangle_other	4.518
r_mcangle_it	3.601
r_mcangle_other	3.601
r_scbond_it	2.852
r_scbond_other	2.85
r_mcbond_it	2.301
r_mcbond_other	2.298
r_angle_refined_deg	1.699
r_angle_other_deg	1.042
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3113
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
SADABS	data reduction
SADABS	data scaling
PHASER	phasing