2C3A

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
14.6100MM NA ACETATE PH 4.6, 10MM ZNCL2, 24% PEG &K
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.629α = 90
b = 79.105β = 90
c = 123.563γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.55099.60.0897.323602-3
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)
12.52.5998.20.345.077.1

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 1L2G2.52522271121299.70.2280.2260.275RANDOM39
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]
1.370.6-1.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.806
r_scangle_it3.412
r_scbond_it2.011
r_angle_refined_deg1.685
r_mcangle_it1.655
r_angle_other_deg0.931
r_mcbond_it0.903
r_symmetry_vdw_refined0.323
r_symmetry_vdw_other0.243
r_nbd_other0.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.806
r_scangle_it3.412
r_scbond_it2.011
r_angle_refined_deg1.685
r_mcangle_it1.655
r_angle_other_deg0.931
r_mcbond_it0.903
r_symmetry_vdw_refined0.323
r_symmetry_vdw_other0.243
r_nbd_other0.235
r_nbd_refined0.206
r_xyhbond_nbd_refined0.174
r_chiral_restr0.105
r_nbtor_other0.09
r_bond_refined_d0.017
r_symmetry_hbond_refined0.007
r_gen_planes_refined0.006
r_gen_planes_other0.005
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 Atoms4067
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing