3DX8 | pdb_00003dx8

Crystal Structure of B*4405 presenting a 10mer EBV epitope

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	Citrate, Ammonium Acetate, PEG 4000, pH 5.6, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.776	α = 90
b = 82.351	β = 90
c = 110.138	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	CCD	MAR CCD 165 mm		2006-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1	APS	17-ID

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	2.1	65.94				26691	26691

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.1	65.94	26691	26568	1344	95.94	0.197	0.197	0.193	0.19	0.255	0.25	RANDOM	29.388

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]
-0.78			-1.19		1.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.698
r_dihedral_angle_4_deg	17.084
r_dihedral_angle_3_deg	14.761
r_dihedral_angle_1_deg	9.507
r_scangle_it	4.959
r_scbond_it	3.894
r_mcangle_it	2.624
r_mcbond_it	2.139
r_angle_refined_deg	1.435
r_angle_other_deg	0.907
r_mcbond_other	0.38
r_symmetry_vdw_other	0.224
r_nbd_other	0.196
r_nbd_refined	0.188
r_nbtor_refined	0.176
r_symmetry_hbond_refined	0.171
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.102
r_symmetry_vdw_refined	0.089
r_nbtor_other	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3178
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling