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PanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z1614545742
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 46.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.35 α = 90 b = 108.9 β = 90 c = 112.07 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 1.66 80.35 100 0.108 0.118 0.046 0.997 10.2 6.5 116537
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 1.66 1.7 100 2.192 2.398 0.964 0.312 6.1 8546
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 1.66 78.1 110736 5700 99.92 0.1896 0.188 0.2004 0.2208 0.2299 RANDOM 29.458
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] 0.91 -0.51 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.734 r_dihedral_angle_3_deg 15.389 r_dihedral_angle_4_deg 15.009 r_dihedral_angle_1_deg 6.848 r_mcangle_it 3.016 r_mcbond_other 2.298 r_mcbond_it 2.296 r_angle_refined_deg 1.592 r_angle_other_deg 1.393 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.734 r_dihedral_angle_3_deg 15.389 r_dihedral_angle_4_deg 15.009 r_dihedral_angle_1_deg 6.848 r_mcangle_it 3.016 r_mcbond_other 2.298 r_mcbond_it 2.296 r_angle_refined_deg 1.592 r_angle_other_deg 1.393 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 524 Heterogen Atoms 183
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing