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Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog
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 7.5 293 PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.88 57.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.59 α = 90 b = 123.478 β = 96.22 c = 164.331 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 0.99187 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 2.86 30 99.6 0.087 10.7 4.4 121231 121231
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) 2.86 2.96 97.3 0.609 2 3.7
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 1RV2 2.86 30 121231 100166 10779 91.18 0.23416 0.22771 0.2265 0.2942 0.2872 RANDOM 74.755
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] -1 2.71 -1.98 3.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.246 r_dihedral_angle_3_deg 17.914 r_dihedral_angle_4_deg 17.467 r_dihedral_angle_1_deg 5.101 r_scangle_it 1.497 r_angle_refined_deg 1.101 r_scbond_it 0.84 r_mcangle_it 0.747 r_mcbond_it 0.401 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.246 r_dihedral_angle_3_deg 17.914 r_dihedral_angle_4_deg 17.467 r_dihedral_angle_1_deg 5.101 r_scangle_it 1.497 r_angle_refined_deg 1.101 r_scbond_it 0.84 r_mcangle_it 0.747 r_mcbond_it 0.401 r_nbtor_refined 0.307 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.181 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.148 r_metal_ion_refined 0.14 r_chiral_restr 0.071 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_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 25760 Nucleic Acid Atoms 2348 Solvent Atoms 651 Heterogen Atoms 130
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data scaling CNS phasing