☰ Navigation Tabs
Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 E88A Mutant
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 293.15 21.43% PEG 6000; 0.1 M Tris; 0.5 M Zinc Chloride
Crystal Properties Matthews coefficient Solvent content 3.33 63.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.63 α = 90 b = 135.63 β = 90 c = 87.56 γ = 120
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 2021-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.89 70.21 99.96 0.294 0.0298 0.999 6.4 38.7 73355
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.92 98.61 5.938 6.026 0.343 0.2 34.7
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.95 44.4 1.34 66760 3239 99.98 0.199 0.1977 0.1994 0.2237 0.2243 RANDOM
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 6.351 f_angle_d 0.873 f_chiral_restr 0.059 f_plane_restr 0.008 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4940 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX phasing xia2 data reduction xia2 data scaling