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Crystal structure of RB69 gp43 in complex with DNA with 5-NITP opposite an abasic site analog
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 7.5 293 PEG 20000,sodium acetate, magnesium acetate, beta-mercaptoethanol, TRIS 7.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.232 α = 90 b = 117.492 β = 90 c = 126.142 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 2.86 30 94.7 0.144 10.3 4.5 28816 28816
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 2.9 71.6 0.374 3
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 THROUGHOUT 1IG9 2.86 30 28786 26082 2704 94.77 0.20977 0.20352 0.1979 0.26836 0.2693 RANDOM 63.807
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] -1.91 -1.54 3.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.698 r_dihedral_angle_4_deg 17.419 r_dihedral_angle_3_deg 16.871 r_dihedral_angle_1_deg 4.935 r_scangle_it 1.539 r_angle_refined_deg 1.072 r_scbond_it 0.87 r_mcangle_it 0.831 r_mcbond_it 0.458 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.698 r_dihedral_angle_4_deg 17.419 r_dihedral_angle_3_deg 16.871 r_dihedral_angle_1_deg 4.935 r_scangle_it 1.539 r_angle_refined_deg 1.072 r_scbond_it 0.87 r_mcangle_it 0.831 r_mcbond_it 0.458 r_nbtor_refined 0.305 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.185 r_metal_ion_refined 0.158 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.102 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_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 7328 Nucleic Acid Atoms 641 Solvent Atoms 400 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection CNS phasing