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Bacillus subtilis cytidine deaminase with an Arg56 - Ala substitution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JTK PDB ENTRY 1JTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 VAPOUR DIFFUSION AT RT: PROTEIN: 4.6 MG/ML + 5 MM TETRAHYDRODEOXYURIDINE PRECIPITANT: 17-23 % MPD,10 MM CALCIUM CHLORIDE, 0.1 M SODIUM ACETATE, pH 4.60
Crystal Properties Matthews coefficient Solvent content 2.1 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.743 α = 90 b = 66.418 β = 115.6 c = 55.388 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 100 CCD MARRESEARCH 2001-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 1.99 20 94 0.114 10.8 4.3 15794 19.1
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 1.99 2.04 54 0.388 1.3
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1JTK 1.99 19.96 15662 747 94.2 0.188 0.188 0.1852 0.211 0.2079 RANDOM 24.6
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] -3.84 0.98 2.65 1.19
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 3.01 c_scbond_it 2.15 c_mcangle_it 1.69 c_angle_deg 1.2 c_mcbond_it 1.11 c_improper_angle_d 0.79 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 3.01 c_scbond_it 2.15 c_mcangle_it 1.69 c_angle_deg 1.2 c_mcbond_it 1.11 c_improper_angle_d 0.79 c_bond_d 0.006 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 1944 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 34
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling