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Crystal structure of dCTP deaminase from Sulfolobus tokodaii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.17M Magnesium Acetate, 0.085M Sodium Cavpdylate pH 6.5, 17% PEG 8000, 0.01M dUTP, 0.01M Magnesium Chloride, 0.02M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.77 α = 107.47 b = 53.757 β = 107.52 c = 53.757 γ = 107.5
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 RIGAKU JUPITER 210 2006-12-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.9789, 0.9794, 0.9000 SPring-8 BL26B2
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 1.6 50 92 0.121 2.7 90293 15.5
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) 1.6 1.66 0.236 2.2 2304
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.66 31.65 40026 8081 77.6 0.208 0.208 0.2127 0.227 0.2347 RANDOM 26.6
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] 0.48 4.62 4.61 -0.14 4.51 -0.34
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26 c_scangle_it 2.21 c_mcangle_it 1.52 c_angle_deg 1.4 c_scbond_it 1.39 c_improper_angle_d 0.96 c_mcbond_it 0.94 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26 c_scangle_it 2.21 c_mcangle_it 1.52 c_angle_deg 1.4 c_scbond_it 1.39 c_improper_angle_d 0.96 c_mcbond_it 0.94 c_bond_d 0.009 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 3753 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 83
Software Software Software Name Purpose CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing