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Structure of Trypanosoma cruzi type B ribose 5-phosphate isomerase (TcRpiB)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 277.15 100mM phosphate citrate pH4.2; 1.6M NaH2PO4/0.4M K2HPO4
Crystal Properties Matthews coefficient Solvent content 72.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.16 α = 90 b = 175.35 β = 90 c = 93.27 γ = 90
Symmetry Space Group C 2 2 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 2015-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.96 47.58 98.8 0.053 26.65 6.4 99426
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.08 96 0.27 6.17
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 MOLECULAR REPLACEMENT THROUGHOUT 3K7O 1.96 47.58 94441 4971 98.81 0.16208 0.16094 0.1746 0.18387 0.1944 RANDOM 23.873
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] 0.33 0.48 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.505 r_dihedral_angle_4_deg 21.645 r_dihedral_angle_3_deg 12.349 r_long_range_B_other 6.891 r_long_range_B_refined 6.889 r_dihedral_angle_1_deg 6.738 r_scangle_other 5.996 r_scbond_it 4.15 r_scbond_other 4.144 r_mcangle_other 3.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.505 r_dihedral_angle_4_deg 21.645 r_dihedral_angle_3_deg 12.349 r_long_range_B_other 6.891 r_long_range_B_refined 6.889 r_dihedral_angle_1_deg 6.738 r_scangle_other 5.996 r_scbond_it 4.15 r_scbond_other 4.144 r_mcangle_other 3.099 r_mcangle_it 3.098 r_mcbond_it 2.433 r_mcbond_other 2.432 r_angle_refined_deg 2.369 r_angle_other_deg 1.192 r_chiral_restr 0.155 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4742 Nucleic Acid Atoms Solvent Atoms 371 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing