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dCTP deaminase from Escherichia coli. E138A mutant enzyme in complex with dUTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XS1 PDB ENTRY 1XS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG 400, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.93 α = 90 b = 63.073 β = 102.18 c = 96.363 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 120 IMAGE PLATE MARRESEARCH 2004-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 25 97.4 0.108 8 3.9 71843 71843
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 2.05 95.5 0.454 2.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1XS1 2 25 66024 3527 97.14 0.26088 0.25809 0.2639 0.31288 0.3155 RANDOM 19.091
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] -0.91 0.64 0.19 0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.204 r_dihedral_angle_4_deg 21.194 r_dihedral_angle_3_deg 15.705 r_dihedral_angle_1_deg 7.131 r_scangle_it 2.544 r_scbond_it 1.702 r_angle_refined_deg 1.593 r_mcangle_it 1.147 r_angle_other_deg 0.903 r_mcbond_it 0.791
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.204 r_dihedral_angle_4_deg 21.194 r_dihedral_angle_3_deg 15.705 r_dihedral_angle_1_deg 7.131 r_scangle_it 2.544 r_scbond_it 1.702 r_angle_refined_deg 1.593 r_mcangle_it 1.147 r_angle_other_deg 0.903 r_mcbond_it 0.791 r_symmetry_hbond_refined 0.261 r_symmetry_vdw_refined 0.224 r_symmetry_vdw_other 0.223 r_nbd_refined 0.2 r_nbd_other 0.192 r_mcbond_other 0.19 r_xyhbond_nbd_refined 0.185 r_xyhbond_nbd_other 0.18 r_metal_ion_refined 0.121 r_chiral_restr 0.089 r_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8952 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing