3SKU

Herpes simplex virus glycoprotein D bound to the human receptor nectin-1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.2	293	1.0 M Na2HPO4/KH2PO4 pH 7.2 and 300 mM NH4SO4, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.66	73.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 188.003	α = 90
b = 188.003	β = 90
c = 185.004	γ = 120

Symmetry
Space Group	P 32 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		2005-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	4	49.1	99.9	0.06	8	2.6		31947		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4	4.1	99.2		0.208	1.7	2.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2C36, 1NEU AND 3ALP	4	30	30529	30227	1675	98.9	0.267	0.266	0.287	RANDOM	151.77

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]
144.41			144.41		-288.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.219
r_dihedral_angle_3_deg	21.664
r_scangle_it	20.5
r_dihedral_angle_4_deg	19.243
r_scbond_it	14.485
r_dihedral_angle_1_deg	8.905
r_mcangle_it	8.412
r_mcbond_it	5.527
r_angle_refined_deg	1.747
r_chiral_restr	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d
r_angle_other_deg
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9592
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	310

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling