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Closed binary complex of an RB69 gp43 fingers domain mutant complexed with an acyclic GMP terminated primer template pair.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IH7 PDB entry 1IH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 5% PEG 20000, 0.1M sodium acetate pH 5, 0.1M magnesium acetate, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.485 α = 90 b = 121.657 β = 90 c = 131.538 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 2.66 50 100 0.106 17.7 7.6 36963 36963
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 2.66 2.76 100 2.24 7.2
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 (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 1IH7 2.66 30 33291 33291 3570 99.96 0.2119 0.20796 0.2037 0.24826 0.2461 RANDOM 41.056
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] -2.73 0.34 2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.214 r_dihedral_angle_3_deg 15.168 r_dihedral_angle_4_deg 14.094 r_dihedral_angle_1_deg 4.505 r_angle_refined_deg 0.916 r_scangle_it 0.75 r_scbond_it 0.412 r_mcangle_it 0.308 r_mcbond_it 0.161 r_chiral_restr 0.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.214 r_dihedral_angle_3_deg 15.168 r_dihedral_angle_4_deg 14.094 r_dihedral_angle_1_deg 4.505 r_angle_refined_deg 0.916 r_scangle_it 0.75 r_scbond_it 0.412 r_mcangle_it 0.308 r_mcbond_it 0.161 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7379 Nucleic Acid Atoms 648 Solvent Atoms 321 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement CNS refinement Blu-Ice data collection DENZO data reduction SCALEPACK data scaling CNS phasing