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Structure of Leishmania infantum 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 277 0.1M Hepes pH7; 2M NH4SO4
Crystal Properties Matthews coefficient Solvent content 2 38.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.92 α = 90 b = 83.65 β = 90 c = 89.49 γ = 90
Symmetry Space Group F 2 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 1.57 19.75 99.6 0.0527 23.2 6.5 21306
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 1.57 1.66 97.8 0.343 5.09
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 1.57 19.75 20240 1066 99.55 0.14611 0.14439 0.1443 0.17829 0.1771 RANDOM 17.348
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] 0.28 0.32 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.657 r_dihedral_angle_4_deg 15.196 r_dihedral_angle_3_deg 12.162 r_dihedral_angle_1_deg 6.22 r_long_range_B_refined 5.701 r_long_range_B_other 5.691 r_scangle_other 4.831 r_scbond_other 3.215 r_scbond_it 3.21 r_mcangle_other 2.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.657 r_dihedral_angle_4_deg 15.196 r_dihedral_angle_3_deg 12.162 r_dihedral_angle_1_deg 6.22 r_long_range_B_refined 5.701 r_long_range_B_other 5.691 r_scangle_other 4.831 r_scbond_other 3.215 r_scbond_it 3.21 r_mcangle_other 2.958 r_mcangle_it 2.947 r_angle_refined_deg 2.217 r_mcbond_it 2.046 r_mcbond_other 1.959 r_angle_other_deg 1.139 r_chiral_restr 0.137 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 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 1149 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing