3FVC | pdb_00003fvc

Crystal structure of a trimeric variant of the Epstein-Barr virus glycoprotein B

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10.5	298	0.1 M N-Cyclohexyl-3-aminopropanesulfonic acid (CAPS) pH 10.5 or 11.5, 1.40 M (NH4)2SO4 (AS) and 0.2 M Li2SO4, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.81	74.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.8	α = 90
b = 106.8	β = 90
c = 210.75	γ = 120

Symmetry
Space Group	P 3 2 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	CCD	MAR CCD 165 mm		2007-05-01		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.0379	APS	5ID-B

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	3.2	50	98.5		8.3		23367

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2		91.6		3	4.8

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2GUM	3.2	26.61	21144	2155	98.36	0.24635	0.24246	0.24	0.28292	0.28	RANDOM	79.778

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]
2.79	1.39		2.79		-4.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.646
r_dihedral_angle_3_deg	23.129
r_dihedral_angle_4_deg	20.633
r_dihedral_angle_1_deg	6.856
r_mcangle_it	1.853
r_scangle_it	1.837
r_angle_refined_deg	1.728
r_scbond_it	1.103
r_mcbond_it	1.074
r_nbtor_refined	0.354
r_symmetry_vdw_refined	0.307
r_symmetry_hbond_refined	0.304
r_nbd_refined	0.3
r_xyhbond_nbd_refined	0.215
r_xyhbond_nbd_other	0.137
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4501
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	42

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection