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PanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z2856434944
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 46.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.06 α = 90 b = 109.06 β = 90 c = 112.05 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 0.91263 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 80.06 100 0.105 0.114 0.044 0.998 10 6.7 85702
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 2.393 2.593 0.989 0.302 6.8 6271
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 56.09 81385 4229 99.91 0.194 0.192 0.2062 0.2323 0.2411 RANDOM 36.802
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] -0.08 0.7 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.207 r_dihedral_angle_3_deg 15.922 r_dihedral_angle_4_deg 12.938 r_dihedral_angle_1_deg 6.945 r_mcangle_it 3.665 r_mcbond_it 2.71 r_mcbond_other 2.706 r_angle_refined_deg 1.518 r_angle_other_deg 1.321 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.207 r_dihedral_angle_3_deg 15.922 r_dihedral_angle_4_deg 12.938 r_dihedral_angle_1_deg 6.945 r_mcangle_it 3.665 r_mcbond_it 2.71 r_mcbond_other 2.706 r_angle_refined_deg 1.518 r_angle_other_deg 1.321 r_chiral_restr 0.073 r_bond_refined_d 0.009 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 538 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing