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Crystal structure of the Herpes Simplex virus type 1 DNA polymerase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 100mM HEPES, 50mM ammonium sulphate, 5mM DTT, 100mM guanidine-HCl, 4% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.917 α = 90 b = 125.55 β = 90 c = 220.577 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2002-11-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0, 0.9794, 0.9504 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.675 48.3 100 0.071 30.2 9.1 81295 81295 4 2.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.675 2.8 100 0.849 2.4 8.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 MAD THROUGHOUT 2.68 48.3 77153 4070 98.88 0.2248 0.22182 0.2209 0.28057 0.2776 RANDOM 52.287
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] -0.64 0.3 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.247 r_dihedral_angle_3_deg 20.681 r_dihedral_angle_4_deg 19.384 r_dihedral_angle_1_deg 7.824 r_scangle_it 2.51 r_angle_refined_deg 1.815 r_scbond_it 1.707 r_mcangle_it 1.137 r_angle_other_deg 1.016 r_mcbond_it 0.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.247 r_dihedral_angle_3_deg 20.681 r_dihedral_angle_4_deg 19.384 r_dihedral_angle_1_deg 7.824 r_scangle_it 2.51 r_angle_refined_deg 1.815 r_scbond_it 1.707 r_mcangle_it 1.137 r_angle_other_deg 1.016 r_mcbond_it 0.918 r_symmetry_vdw_other 0.317 r_nbd_refined 0.249 r_nbd_other 0.208 r_nbtor_refined 0.198 r_xyhbond_nbd_refined 0.18 r_symmetry_hbond_refined 0.167 r_symmetry_vdw_refined 0.154 r_mcbond_other 0.137 r_chiral_restr 0.099 r_nbtor_other 0.097 r_xyhbond_nbd_other 0.029 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 15905 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling SHELXS phasing