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crystal structure of Uracil-DNA glycosylase from Atlantic cod (Gadus morhua)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AKZ PDB ENTRY 1AKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M HEPES PH 7.5, 1.4M SODIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 2.71 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.58 α = 90 b = 67.189 β = 119.86 c = 68.644 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 120 IMAGE PLATE MAR scanner 345 mm plate 2001-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM1A ESRF BM1A
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 1.9 12 98.7 0.096 10.2 3.3 42162 19.45
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) 1 1.9 2 97.5 0.522 2 2.9
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1AKZ 1.9 12 42162 2112 98.7 0.1861 0.1861 0.2057 RANDOM 22.4043
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] 1.623 2.017 -3.129 1.506
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.207 c_scangle_it 3.184 c_scbond_it 2.125 c_mcangle_it 2.003 c_mcbond_it 1.291 c_angle_deg 1.189 c_improper_angle_d 0.832 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.207 c_scangle_it 3.184 c_scbond_it 2.125 c_mcangle_it 2.003 c_mcbond_it 1.291 c_angle_deg 1.189 c_improper_angle_d 0.832 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3574 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 14
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALA data scaling CNS phasing