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Bacillus cereus DNA glycosylase AlkD bound to a duocarmycin SA-adenine nucleobase adduct and DNA containing an abasic site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BVS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 24% (w/v) PEG 8000, 50 mM HEPES pH 7.0, and 50 mM calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.27 45.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.715 α = 90 b = 55.661 β = 112.2 c = 47.991 γ = 90
Symmetry Space Group C 1 2 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 RAYONIX MX-300 2018-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.93 50 99.9 0.067 0.073 0.028 10.9 6.3 22584
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 2.01 98.8 0.598 0.654 0.259 0.836 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3BVS 1.93 44.434 1.35 22575 1132 97.99 0.1564 0.1539 0.156 0.2012 0.2018 RANDOM 45.5047
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.811 f_angle_d 1.116 f_chiral_restr 0.059 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1923 Nucleic Acid Atoms 354 Solvent Atoms 189 Heterogen Atoms 75
Software Software Software Name Purpose HKL-2000 data reduction DENZO data reduction HKL-2000 data scaling SCALEPACK data scaling PHENIX phasing PHASER phasing Coot model building PHENIX refinement PDB_EXTRACT data extraction