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Arsenic treated Treponema pallidum thioredoxin strain Nichols
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9NCE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.15 M DL-Malic acid pH 7.0, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.04 39.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.624 α = 90 b = 48.624 β = 90 c = 91.989 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2017-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953728 Australian Synchrotron MX2
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 1.7 31.1 99.6 0.059 0.064 0.024 0.999 16 6.9 13484
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 1.7 1.73 95 0.742 0.806 0.31 0.894 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 1.7 31.08 12774 673 99.72 0.17131 0.16882 0.1829 0.21376 0.2213 RANDOM 34.896
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] 0.82 0.41 0.82 -2.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.372 r_dihedral_angle_2_deg 8.338 r_long_range_B_refined 6.832 r_long_range_B_other 6.787 r_dihedral_angle_1_deg 5.95 r_scangle_other 5.459 r_scbond_it 3.969 r_scbond_other 3.965 r_mcangle_other 3.357 r_mcangle_it 3.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.372 r_dihedral_angle_2_deg 8.338 r_long_range_B_refined 6.832 r_long_range_B_other 6.787 r_dihedral_angle_1_deg 5.95 r_scangle_other 5.459 r_scbond_it 3.969 r_scbond_other 3.965 r_mcangle_other 3.357 r_mcangle_it 3.354 r_mcbond_it 2.676 r_mcbond_other 2.676 r_angle_refined_deg 2.129 r_angle_other_deg 0.717 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 806 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing