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PanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z1899842917
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 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.98 α = 90 b = 109.24 β = 90 c = 112.13 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 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 1.84 78.25 100 0.099 0.108 0.042 0.998 10.8 6.7 85835
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 1.84 1.89 100 2.552 2.763 1.054 0.297 6.8 6279
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 1.84 78.25 81508 4240 99.92 0.1967 0.1946 0.2151 0.2381 0.2511 RANDOM 39.025
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] -0.62 1.35 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.892 r_dihedral_angle_3_deg 15.461 r_dihedral_angle_4_deg 14.263 r_dihedral_angle_1_deg 7.036 r_mcangle_it 3.803 r_mcbond_other 2.825 r_mcbond_it 2.822 r_angle_refined_deg 1.483 r_angle_other_deg 1.305 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.892 r_dihedral_angle_3_deg 15.461 r_dihedral_angle_4_deg 14.263 r_dihedral_angle_1_deg 7.036 r_mcangle_it 3.803 r_mcbond_other 2.825 r_mcbond_it 2.822 r_angle_refined_deg 1.483 r_angle_other_deg 1.305 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7360 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing