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Structure of Trypanosoma brucei type B ribose 5-phosphate isomerase
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 295 100mM hepes pH7.5; 1.26M NH4SO4
Crystal Properties Matthews coefficient Solvent content 2.62 53.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.8 α = 90 b = 97.8 β = 90 c = 84.18 γ = 90
Symmetry Space Group P 41 2 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 PIXEL DECTRIS PILATUS 6M 2015-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.912 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 2.01 19.56 99.8 0.111 22.12 12.7 27783
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 2.01 2.13 99.5 0.627 4.45
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 2.01 19.56 26392 1390 99.76 0.16565 0.16394 0.1767 0.19774 0.2061 RANDOM 23.882
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] 0.17 0.17 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.429 r_dihedral_angle_4_deg 23.76 r_dihedral_angle_3_deg 13.442 r_long_range_B_refined 6.809 r_long_range_B_other 6.792 r_scangle_other 5.834 r_dihedral_angle_1_deg 5.638 r_scbond_it 3.918 r_scbond_other 3.915 r_mcangle_other 2.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.429 r_dihedral_angle_4_deg 23.76 r_dihedral_angle_3_deg 13.442 r_long_range_B_refined 6.809 r_long_range_B_other 6.792 r_scangle_other 5.834 r_dihedral_angle_1_deg 5.638 r_scbond_it 3.918 r_scbond_other 3.915 r_mcangle_other 2.939 r_mcangle_it 2.936 r_mcbond_it 2.147 r_mcbond_other 2.142 r_angle_refined_deg 2.102 r_angle_other_deg 1.125 r_chiral_restr 0.123 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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 2296 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing