2GV9

Crystal structure of the Herpes Simplex virus type 1 DNA polymerase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7100mM HEPES, 50mM ammonium sulphate, 5mM DTT, 100mM guanidine-HCl, 4% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.6353.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.917α = 90
b = 125.55β = 90
c = 220.577γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152002-11-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0, 0.9794, 0.9504APS17-ID

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
12.67548.31000.07130.29.1812958129542.4
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)
12.6752.81000.8492.48.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.6848.377153407098.880.22480.221820.28057RANDOM52.287
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]
-0.640.30.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.247
r_dihedral_angle_3_deg20.681
r_dihedral_angle_4_deg19.384
r_dihedral_angle_1_deg7.824
r_scangle_it2.51
r_angle_refined_deg1.815
r_scbond_it1.707
r_mcangle_it1.137
r_angle_other_deg1.016
r_mcbond_it0.918
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.247
r_dihedral_angle_3_deg20.681
r_dihedral_angle_4_deg19.384
r_dihedral_angle_1_deg7.824
r_scangle_it2.51
r_angle_refined_deg1.815
r_scbond_it1.707
r_mcangle_it1.137
r_angle_other_deg1.016
r_mcbond_it0.918
r_symmetry_vdw_other0.317
r_nbd_refined0.249
r_nbd_other0.208
r_nbtor_refined0.198
r_xyhbond_nbd_refined0.18
r_symmetry_hbond_refined0.167
r_symmetry_vdw_refined0.154
r_mcbond_other0.137
r_chiral_restr0.099
r_nbtor_other0.097
r_xyhbond_nbd_other0.029
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms15905
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data scaling
SHELXSphasing