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Crystal structure of RB69 gp43 in complex with DNA with dATP opposite dTMP
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 7 293 PEG 20000, sodium acetate, magnesium acetate, beta-mercaptoethanol, TRIS 7.0, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.69 54.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.306 α = 90 b = 117.754 β = 90 c = 129.133 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 225 mm CCD 2005-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.873 ESRF BM14
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 2.75 50 94.9 0.148 10.1 4.1 31271 31271
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) 2.75 2.85 73.1 0.341 2.7 2.6 2348
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 1IG9 2.75 30 30422 2641 92.53 0.221 0.216 0.1989 0.272 0.2582 COPIED FROM 1IG9 53.334
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] -3.22 -3.24 6.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.691 r_dihedral_angle_3_deg 17.532 r_dihedral_angle_4_deg 14.779 r_dihedral_angle_1_deg 5.614 r_scangle_it 3.845 r_scbond_it 2.813 r_mcangle_it 1.652 r_angle_refined_deg 1.389 r_mcbond_it 1.032 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.691 r_dihedral_angle_3_deg 17.532 r_dihedral_angle_4_deg 14.779 r_dihedral_angle_1_deg 5.614 r_scangle_it 3.845 r_scbond_it 2.813 r_mcangle_it 1.652 r_angle_refined_deg 1.389 r_mcbond_it 1.032 r_nbtor_refined 0.312 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.153 r_metal_ion_refined 0.14 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7350 Nucleic Acid Atoms 650 Solvent Atoms 283 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing