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Co- and Bi-bound structure of the H77C variant of TriCyt2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 25% PEG 1500, 200 mM CaCl2,
100 mM HEPES (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.09 41.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.54 α = 90 b = 71.09 β = 90 c = 75.44 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2022-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.928 ALS 5.0.2
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 43.77 99.85 0.05231 0.05699 0.02229 0.999 23.37 6.4 38593 29.87
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 2.003 2.075 99.75 0.4227 0.4637 0.1878 0.895 4.02
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 43.77 1.96 38593 3732 99.45 0.222 0.2182 0.2569 0.2699 36.27
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 9.9776 f_angle_d 0.3621 f_chiral_restr 0.032 f_plane_restr 0.0032 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2499 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 3
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing