3FD4 | pdb_00003fd4

Crystal Structure of Epstein-Barr virus gp42 protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KG0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	9.5	298	30% PEG-3000, 100 mM CHES pH 9.5, 10 mM YCl3, 25 mM tris pH 7.5, 150 mM NaCl, temperature 298K, VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.792	α = 90
b = 67.469	β = 90
c = 79.463	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	MARMOSAIC 300 mm CCD		2007-03-26		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID		APS	22-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	2.4	46.73	99.4			14237	14139	4.4	4.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.49	99.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1KG0	2.4	46.73	14237	13445	629	99.55	0.21666	0.21548	0.21	0.24226	0.24	RANDOM	37.86

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]
-3.99			-2.34		6.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.37
r_dihedral_angle_4_deg	38.216
r_dihedral_angle_3_deg	19.621
r_dihedral_angle_1_deg	7.13
r_scangle_it	4.939
r_mcangle_it	4.342
r_scbond_it	3.308
r_mcbond_it	2.778
r_angle_refined_deg	1.708
r_mcbond_other	0.794
r_symmetry_vdw_refined	0.225
r_xyhbond_nbd_refined	0.215
r_symmetry_vdw_other	0.202
r_nbtor_refined	0.183
r_nbd_other	0.18
r_symmetry_hbond_refined	0.168
r_nbd_refined	0.163
r_nbtor_other	0.159
r_chiral_restr	0.116
r_bond_refined_d	0.026
r_gen_planes_refined	0.009
r_gen_planes_other	0.005
r_bond_other_d
r_angle_other_deg
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2318
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling