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Tryparedoxin from Trypanosoma brucei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QK8 PDB ENTRY 1QK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 50 MM HEPES PH 7.5, 30% PEG4000, 100 MM SODIUM ACETATE PH 4.6, 200 MM AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.6 α = 90 b = 31.46 β = 93.43 c = 56.93 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 IMAGE PLATE RIGAKU IMAGE PLATE ROTATING ANODE M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.28 56.8 98.7 0.073 19.6 8.1 5030 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.36 94.7 0.217 6.5 3.4
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QK8 2.28 56.8 4794 229 98.6 0.177 0.1966 0.244 0.2382 RANDOM 26.62
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] 1.28 0.45 -0.95 -0.28
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.995 r_scbond_it 4.271 r_angle_refined_deg 3.04 r_mcangle_it 2.854 r_mcbond_it 1.824 r_angle_other_deg 1.361 r_symmetry_vdw_other 0.328 r_nbd_other 0.247 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.217
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.995 r_scbond_it 4.271 r_angle_refined_deg 3.04 r_mcangle_it 2.854 r_mcbond_it 1.824 r_angle_other_deg 1.361 r_symmetry_vdw_other 0.328 r_nbd_other 0.247 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.217 r_chiral_restr 0.207 r_symmetry_vdw_refined 0.146 r_nbtor_other 0.11 r_symmetry_hbond_refined 0.085 r_bond_refined_d 0.049 r_gen_planes_refined 0.02 r_gen_planes_other 0.019 r_bond_other_d 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1124 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing