☰ Navigation Tabs
Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 WT bound to Bis-Tris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F62 experimental model PDB 3EHD experimental model PDB 6EVS experimental model PDB 6QAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 9.8 mg/ml enzyme; 22.5% v/v PEG Smear Broad; 0.1 M Bis-Tris pH 7.5; 0.05 M Zinc acetate dihydrate; 0.2 M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.16 61.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.189 α = 90 b = 131.189 β = 90 c = 86.94 γ = 120
Symmetry Space Group P 62 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 298 PIXEL DECTRIS EIGER2 XE 16M 2021-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.7 113.61 100 0.145 0.146 0.02 1 19.6 50.9 48818
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 100 1.626 1.654 0.299 0.955 1.3 29.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 69.04 1.35 48768 2485 99.97 0.1923 0.1905 0.1988 0.2251 0.2327
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 16.273 f_angle_d 1.708 f_chiral_restr 0.062 f_bond_d 0.042 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2413 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement PHENIX phasing xia2 data reduction xia2 data scaling