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Crystal Structure of Mouse Cytidine Deaminase Complexed with Cytidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FR5 PDB ENTRY 2FR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 0.9M AMMONIUM SULPHATE, 0.1M CITRATE, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.199 α = 90 b = 92.961 β = 90 c = 180.737 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2004-03-28 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 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 2.07 33.59 100 0.079 11.4 4.6 42537 42537 17
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) 2.07 2.14 99.9 99.9 0.345 3.9 4.53 4184
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 2FR5 2.07 33.59 42417 42417 2130 99.5 0.188 0.1812 0.214 0.2032 RANDOM 25.6
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] -1 4.97 -3.97
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 2.84 c_scbond_it 2.23 c_mcangle_it 1.71 c_angle_deg 1.4 c_mcbond_it 1.14 c_improper_angle_d 1 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4255 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 78
Software Software Software Name Purpose d*TREK data scaling CNS refinement PDB_EXTRACT data extraction