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PANDDA analysis - Crystal structure of Trypanosoma brucei trypanothione reductase in complex with Z2017861827
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 12-14% PEG3350, 22-24% MPD, 40 mM imidazole pH 8.0, 50 mM NaBr
Crystal Properties Matthews coefficient Solvent content 2.58 52.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.234 α = 90 b = 63.906 β = 97.67 c = 170.532 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 9M 2022-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.921237 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.62 101.52 99.6 1 9.9 6.9 276971 27.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.65 95.9 0.3 0.4 6.1
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 1.62 84.5 1.33 276539 13743 99.41 0.1982 0.1968 0.1968 0.224 0.224 32.89
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 15.4883 f_angle_d 0.8468 f_chiral_restr 0.059 f_bond_d 0.0071 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14817 Nucleic Acid Atoms Solvent Atoms 919 Heterogen Atoms 286
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling REFMAC phasing