3SKU | pdb_00003sku

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

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C36	2C36, 1NEU AND 3ALP
experimental model	PDB	1NEU	2C36, 1NEU AND 3ALP
experimental model	PDB	3ALP	2C36, 1NEU AND 3ALP

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.27	0.287	0.28	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