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Crystal structure of RB69 gp43 in complex with DNA with dAMP opposite an abasic site analog in a 21mer template
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.628 α = 90 b = 122.272 β = 96.45 c = 163.871 γ = 90
Symmetry Space Group P 1 21 1
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 mirrors 2006-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97857 APS 23-ID-D
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 2.8 50 98.5 0.085 14.3 3.4 125168 125168
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) 2.8 2.9 87.7 0.402 2.6 3.2
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 Isomorphous Replacement THROUGHOUT 1RV2 2.8 30 101465 10837 88.41 0.24013 0.23422 0.2368 0.29524 0.2936 RANDOM 73.922
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] -0.03 3.35 -1.66 2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.238 r_dihedral_angle_3_deg 17.767 r_dihedral_angle_4_deg 17.381 r_dihedral_angle_1_deg 5.042 r_scangle_it 1.484 r_angle_refined_deg 1.062 r_scbond_it 0.902 r_mcangle_it 0.788 r_mcbond_it 0.477 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.238 r_dihedral_angle_3_deg 17.767 r_dihedral_angle_4_deg 17.381 r_dihedral_angle_1_deg 5.042 r_scangle_it 1.484 r_angle_refined_deg 1.062 r_scbond_it 0.902 r_mcangle_it 0.788 r_mcbond_it 0.477 r_nbtor_refined 0.304 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26440 Nucleic Acid Atoms 2336 Solvent Atoms 403 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection CNS phasing