☰ Navigation Tabs
Crystal structure of a plant cytidine deaminase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293.15 0.0085 M CoCl2, 0.085 sodium acetate pH 4.6, 0.85 M 1,6-hexanediol, 15% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 3 58.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.808 α = 90 b = 99.808 β = 90 c = 143.061 γ = 90
Symmetry Space Group P 43 21 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 RAYONIX MX300HE Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips 2015-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.1 47.67 97.9 0.08 0.997 9.7 2.4 41687 31.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 95 0.607 0.622 2 3267
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2B3J 2.101 44.635 1.33 37797 1952 97.62 0.1822 0.1806 0.1836 0.2136 0.181 51.2129
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.607 f_angle_d 0.5 f_chiral_restr 0.043 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3533 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 122
Software Software Software Name Purpose PHENIX refinement PHASER phasing PDB_EXTRACT data extraction Aimless data scaling Coot model building XDS data reduction