2C36

Structure of unliganded HSV gD reveals a mechanism for receptor- mediated activation of virus entry


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L2GPDB ENTRY 1L2G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
160.1M NA-CACODYLATE PH 6.0, 100MM NACL, 100UM ZNAC2, 20% PEG 4K
Crystal Properties
Matthews coefficientSolvent content
3.867.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.252α = 90
b = 106.193β = 90
c = 130.315γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-DAPS14-BM-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.181.6592.50.0614.44.3557702
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1878.10.422.83.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1L2G2.1181.6552889281692.40.1970.1940.247RANDOM40.85
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]
3.850.96-4.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.681
r_scangle_it3.166
r_scbond_it1.812
r_angle_refined_deg1.523
r_mcangle_it1.484
r_angle_other_deg1.059
r_mcbond_it0.794
r_symmetry_vdw_other0.276
r_symmetry_hbond_refined0.242
r_nbd_other0.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.681
r_scangle_it3.166
r_scbond_it1.812
r_angle_refined_deg1.523
r_mcangle_it1.484
r_angle_other_deg1.059
r_mcbond_it0.794
r_symmetry_vdw_other0.276
r_symmetry_hbond_refined0.242
r_nbd_other0.237
r_nbd_refined0.192
r_xyhbond_nbd_refined0.157
r_symmetry_vdw_refined0.15
r_chiral_restr0.087
r_nbtor_other0.087
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4282
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing