☰ Navigation Tabs
Tryparedoxin from Trypanosoma brucei in complex with CFT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 1.045 M Na-citrate, 0.1 M Na-acetate
Crystal Properties Matthews coefficient Solvent content 1.87 34.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.63 α = 90 b = 96.009 β = 96.57 c = 48.276 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 S 6M 2017-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.980004 ESRF ID23-1
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 1.8 50 97.2 0.141 0.163 0.079 0.99 6.9 4 32420
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 1.8 1.83 90.2 0.624 0.722 0.354 0.685 1.8 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1o73 1.8 20 30805 1564 96.98 0.16771 0.16542 0.21217 0.2113 RANDOM 20.198
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] -0.51 0.66 0.09 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.931 r_dihedral_angle_4_deg 12.443 r_dihedral_angle_3_deg 12.234 r_dihedral_angle_1_deg 6.417 r_long_range_B_refined 5.98 r_long_range_B_other 5.633 r_angle_other_deg 3.745 r_scangle_other 2.487 r_mcangle_other 2.109 r_mcangle_it 2.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.931 r_dihedral_angle_4_deg 12.443 r_dihedral_angle_3_deg 12.234 r_dihedral_angle_1_deg 6.417 r_long_range_B_refined 5.98 r_long_range_B_other 5.633 r_angle_other_deg 3.745 r_scangle_other 2.487 r_mcangle_other 2.109 r_mcangle_it 2.108 r_scbond_it 1.596 r_scbond_other 1.596 r_angle_refined_deg 1.375 r_mcbond_it 1.325 r_mcbond_other 1.323 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 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 3392 Nucleic Acid Atoms Solvent Atoms 624 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing