☰ Navigation Tabs
Crystal Structure of Mouse Cytidine Deaminase Complexed with Tetrahydrouridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MQ0 PDB ENTRY 1MQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 298 0.8M AMMONIUM SULPHATE, 0.1M CITRATE, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.69 54.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.238 α = 90 b = 93.403 β = 90 c = 180.743 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 0.9 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 1.48 41.49 96.7 0.073 15.6 6.63 111799 111799
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 1.48 1.53 98.9 98.9 0.288 5 5.26 11283
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 (All) 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 1MQ0 1.48 41.49 111795 111795 5592 96.66 0.169 0.169 0.168 0.1668 0.19 0.1903 RANDOM 13.577
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] -0.33 0.71 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.392 r_dihedral_angle_4_deg 13.548 r_dihedral_angle_3_deg 12.394 r_dihedral_angle_1_deg 5.73 r_angle_refined_deg 1.447 r_scangle_it 1.414 r_scbond_it 1.026 r_mcangle_it 0.745 r_mcbond_it 0.481 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.392 r_dihedral_angle_4_deg 13.548 r_dihedral_angle_3_deg 12.394 r_dihedral_angle_1_deg 5.73 r_angle_refined_deg 1.447 r_scangle_it 1.414 r_scbond_it 1.026 r_mcangle_it 0.745 r_mcbond_it 0.481 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.256 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4186 Nucleic Acid Atoms Solvent Atoms 498 Heterogen Atoms 77
Software Software Software Name Purpose d*TREK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction BBS data reduction