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Crystal Structure of Mouse Cytidine Deaminase Complexed with 3-Deazauridine
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 Ammonium sulphate, citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.7 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.237 α = 90 b = 92.361 β = 90 c = 180.531 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 CCD RIGAKU JUPITER 210 2004-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0 SPring-8 BL26B2
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 48.56 99.4 0.095 9.8 5.21 28544 28544 15.2
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) 2.36 2.44 100 0.29 4.4 5.28 2834
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-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2FR5 2.36 48.56 28184 28184 1368 98 0.178 0.176 0.206 0.1849 RANDOM 23.2
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] -0.52 6.01 -5.49
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 3.09 c_scbond_it 2.35 c_mcangle_it 1.87 c_angle_deg 1.3 c_mcbond_it 1.18 c_improper_angle_d 0.79 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4252 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 77
Software Software Software Name Purpose CNS refinement BBS data reduction CrystalClear data scaling MOLREP phasing