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Crystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IG9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 297 3% PEG 20000, 100mM sodium acetate, 100mM manganese acetate, 100mM Tris-HCl, 1% glycerol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.011 α = 90 b = 121.002 β = 90 c = 128.668 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 MARMOSAIC 300 mm CCD 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3 26810
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 1IG9 3 29.82 22682 1147 91.84 0.24407 0.24153 0.2076 0.29496 0.2753 RANDOM 94.211
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] -12.42 7.63 4.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.263 r_dihedral_angle_3_deg 18.828 r_dihedral_angle_4_deg 14.366 r_dihedral_angle_1_deg 5.472 r_angle_refined_deg 1.16 r_chiral_restr 0.077 r_mcbond_it 0.03 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.263 r_dihedral_angle_3_deg 18.828 r_dihedral_angle_4_deg 14.366 r_dihedral_angle_1_deg 5.472 r_angle_refined_deg 1.16 r_chiral_restr 0.077 r_mcbond_it 0.03 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7371 Nucleic Acid Atoms 652 Solvent Atoms 11 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing