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Closed ternary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair and phosphonoformic acid.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KD1 PDB entry 3KD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 5% PEG 20000, 0.1M sodium acetate pH5, 0.1M magnesium acetate, 0.1M Tris HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.75 55.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.855 α = 90 b = 122.481 β = 90 c = 133.371 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 200 IMAGE PLATE MAR scanner 300 mm plate Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geomet
ry 2009-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03315 APS 23-ID-B
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 2.7 40 100 0.113 26.9 23.4 36065 36065 86.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 100 3.4 21.1 3545
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 3KD1 2.69 30 32507 32507 3470 99.23 0.21939 0.21939 0.21467 0.2176 0.26317 0.2603 Test set extracted from 1IG9 38.787
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] -5.64 0.5 5.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.671 r_dihedral_angle_3_deg 16.703 r_dihedral_angle_4_deg 14.732 r_dihedral_angle_1_deg 4.732 r_angle_refined_deg 0.958 r_chiral_restr 0.067 r_mcbond_it 0.023 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7379 Nucleic Acid Atoms 648 Solvent Atoms 246 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CNS refinement Blu-Ice data collection DENZO data reduction SCALEPACK data scaling CNS phasing