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Bacillus subtilis cytidine deaminase with a Cys53His and an Arg56Gln 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 7.5 VAPOUR DIFFUSION AT RT: PROTEIN: 4.6 MG/ML, + 5 MM TETRAHYDRODEOXYURIDINE, PRECIPITANT: 30 % PEG400, 0.2M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.484 α = 90 b = 62.484 β = 90 c = 221.604 γ = 120
Symmetry Space Group P 32 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 OSMIC MIRRORS 2002-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.36 25 98.9 0.059 29.8 6.8 21401 28.3
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 2.36 2.41 83.9 0.217 6.9
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 1JTK 2.36 24.66 21345 1071 99.4 0.213 0.213 0.2127 0.245 0.2106 RANDOM 32.6
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] -0.96 0.34 -0.96 1.92
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 3.16 c_mcangle_it 2.29 c_scbond_it 2.16 c_mcbond_it 1.39 c_angle_deg 1.2 c_improper_angle_d 0.77 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 3.16 c_mcangle_it 2.29 c_scbond_it 2.16 c_mcbond_it 1.39 c_angle_deg 1.2 c_improper_angle_d 0.77 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 3940 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 76
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling EPMR phasing