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Nucleoside 2'deoxyribosyltransferase from Chroococcidiopsis thermalis PCC 7203 Y7F Mutant bound to ImmH-Forodesine
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 0.1 M Tris pH 8.0, 0.002 M Zinc chloride, 20% w/v PEG6000
Crystal Properties Matthews coefficient Solvent content 3.31 62.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.76 α = 90 b = 135.76 β = 90 c = 87.55 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 2022-05-31 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 2.44 70.21 99.12 0.16 0.165 0.038 0.997 9.4 16.1 33966
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 2.44 2.48 1.833 2.036 0.859 0.295 0.3
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 2.51 48.8 1.34 31437 1561 99.75 0.2126 0.2102 0.2097 0.2627 0.2608 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 16.129 f_angle_d 0.622 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4957 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 38
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHENIX phasing