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Bacillus cereus DNA glycosylase AlkD bound to a yatakemycin-adenine nucleobase adduct and DNA containing an abasic site (9-mer product complex)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BVS PDB entry 3BVS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 25% PEG8000, 50 mM HEPES, pH 7.0, 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 MARMOSAIC 300 mm CCD 2015-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 1.71 50 100 0.084 0.091 0.036 10.6 6.5 32871 17.89
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 1.71 1.77 100 0.577 0.634 0.259 0.877 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 3BVS 1.712 44.434 1.34 32863 1646 99.88 0.1383 0.1362 0.1418 0.1769 0.1793 27.6548
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 18.102 f_angle_d 1.313 f_chiral_restr 0.054 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1923 Nucleic Acid Atoms 354 Solvent Atoms 391 Heterogen Atoms 94
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling PHENIX refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling