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KSHV uracil-DNA glycosylase, product complex with dsDNA exhibiting duplex nucleotide flipping
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 289 0.1 M sodium acetate, 0.1 M magnesium acetate, 8% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.1 59.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.1 α = 90 b = 70.8 β = 94.36 c = 140.25 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 PIXEL PSI PILATUS 6M 2015-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 2.97 73.09 100 0.151 0.144 0.971 6.7 3.4 33476
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.97 9.85 100 0.694 0.65 0.656 1.9 3.4
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 MOLECULAR REPLACEMENT THROUGHOUT 2J8X 2.97 49.2 32502 1717 96.96 0.2451 0.2438 0.239 0.2692 0.2643 RANDOM 73.1692
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] -2.56 -0.19 1.17 1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.234 r_dihedral_angle_4_deg 18.673 r_dihedral_angle_3_deg 16.916 r_mcangle_it 5.827 r_mcbond_it 4.249 r_mcbond_other 4.186 r_angle_other_deg 4 r_dihedral_angle_1_deg 2.554 r_angle_refined_deg 1.664 r_chiral_restr 0.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.234 r_dihedral_angle_4_deg 18.673 r_dihedral_angle_3_deg 16.916 r_mcangle_it 5.827 r_mcbond_it 4.249 r_mcbond_other 4.186 r_angle_other_deg 4 r_dihedral_angle_1_deg 2.554 r_angle_refined_deg 1.664 r_chiral_restr 0.158 r_bond_refined_d 0.015 r_gen_planes_other 0.013 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6954 Nucleic Acid Atoms 1760 Solvent Atoms 111 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction MOLREP phasing Aimless data scaling