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PanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z2856434898
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RB5 6RB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 MPD 22%, PEG 3350 14%, imidazole 40 mM pH 8
Crystal Properties Matthews coefficient Solvent content 2.28 46.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.282 α = 90 b = 108.597 β = 90 c = 111.946 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 PILATUS 6M 2021-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9126 Diamond I04-1
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 1.8 80.28 100 0.133 0.145 0.056 0.997 8.2 6.6 91672
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 1.8 1.89 100 2.1 2.272 0.863 0.409 6.8 13227
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 6RB5 1.8 77.95 86893 4486 99.66 0.2038 0.2018 0.2116 0.2437 0.2496 RANDOM 33.764
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] 1.71 -0.65 -1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.882 r_dihedral_angle_4_deg 14.967 r_dihedral_angle_3_deg 14.696 r_dihedral_angle_1_deg 7.151 r_mcangle_it 3.223 r_mcbond_other 2.379 r_mcbond_it 2.374 r_angle_refined_deg 1.507 r_angle_other_deg 1.317 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.882 r_dihedral_angle_4_deg 14.967 r_dihedral_angle_3_deg 14.696 r_dihedral_angle_1_deg 7.151 r_mcangle_it 3.223 r_mcbond_other 2.379 r_mcbond_it 2.374 r_angle_refined_deg 1.507 r_angle_other_deg 1.317 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7360 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 171
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing