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Marpharsen 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 0.2 M Nacl, 0.1M Na+/K+ phosphate 6.2, 50 % v/v PEG 200
Crystal Properties Matthews coefficient Solvent content 2.26 45.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.05 α = 90 b = 89.05 β = 90 c = 35.176 γ = 90
Symmetry Space Group P 43 21 2
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 2012-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.918400 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 2.64 44.53 99.4 0.048 0.051 0.018 0.999 33.6 8.6 4498
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 2.64 2.76 99.8 0.543 0.582 0.203 0.954 8.6
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 2.64 39.86 4240 220 98.89 0.21116 0.20892 0.2231 0.25464 0.2615 RANDOM 58.951
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] -4.03 -4.03 8.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.531 r_dihedral_angle_2_deg 12.525 r_dihedral_angle_1_deg 7.895 r_long_range_B_refined 7.233 r_long_range_B_other 7.229 r_scangle_other 6.065 r_mcangle_it 4.543 r_mcangle_other 4.539 r_scbond_it 3.873 r_scbond_other 3.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.531 r_dihedral_angle_2_deg 12.525 r_dihedral_angle_1_deg 7.895 r_long_range_B_refined 7.233 r_long_range_B_other 7.229 r_scangle_other 6.065 r_mcangle_it 4.543 r_mcangle_other 4.539 r_scbond_it 3.873 r_scbond_other 3.868 r_mcbond_it 3.041 r_mcbond_other 3.041 r_angle_refined_deg 1.733 r_angle_other_deg 0.567 r_chiral_restr 0.08 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 791 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing