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Crystal structure of 2'-deoxycytidine 5'-triphosphate deaminase from Agrobacterium tumefaciens
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 0.2M CaCl2, 20% PEG 3350, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.29 46.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.693 α = 90 b = 129.042 β = 108.75 c = 85.559 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 100 CCD ADSC QUANTUM 315 mirrors 2007-08-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97940, 0.97960 APS 19-ID
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 2.2 46.78 93.9 0.099 17.1 4.1 73588 69099 2 57
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 2.2 2.26 53.36 0.647 0.8 1.7 5433
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 2.2 46.78 69099 69099 690 93.9 0.1898 0.1898 0.18904 0.2178 0.26949 0.2926 RANDOM 56.968
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] 0.19 -0.38 -0.12 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.399 r_dihedral_angle_4_deg 17.045 r_dihedral_angle_3_deg 16.596 r_dihedral_angle_1_deg 7.218 r_scangle_it 3.741 r_scbond_it 2.579 r_mcangle_it 1.851 r_angle_refined_deg 1.521 r_mcbond_it 1.153 r_angle_other_deg 1.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.399 r_dihedral_angle_4_deg 17.045 r_dihedral_angle_3_deg 16.596 r_dihedral_angle_1_deg 7.218 r_scangle_it 3.741 r_scbond_it 2.579 r_mcangle_it 1.851 r_angle_refined_deg 1.521 r_mcbond_it 1.153 r_angle_other_deg 1.057 r_mcbond_other 0.355 r_nbd_other 0.207 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.18 r_symmetry_vdw_other 0.18 r_xyhbond_nbd_other 0.174 r_nbtor_refined 0.172 r_symmetry_vdw_refined 0.17 r_symmetry_hbond_refined 0.11 r_chiral_restr 0.088 r_nbtor_other 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10146 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling SOLVE phasing