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The Crystal Structure of Cytidine Deaminase CDD1, an Orphan C to U editase from Yeast
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 PEG 5000 MME, ammonium chloride, sodium succinate, DTT, sodium azide, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.52 α = 90 b = 86.37 β = 90 c = 156.26 γ = 90
Symmetry Space Group C 2 2 21
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 APS-1 Vertical Focusing Mirrors 2001-09-17 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.2574, 1.2831, 1.2828 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2 29 91.5 0.064 17.7 4.5 65372 63560 -3 29.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 74.8 0.313 2.1 4.5 5597
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2 29.05 65372 63560 5026 91.5 0.191 0.188 0.188 0.1924 0.222 0.2266 RANDOM 37.2
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] 2.21 2.82 -5.03
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.9 c_scangle_it 3.99 c_mcangle_it 2.75 c_scbond_it 2.28 c_mcbond_it 1.35 c_angle_deg 1.2 c_improper_angle_d 0.72 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4195 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 4
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing SHELX phasing DM phasing O model building