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Crystal structure of Trypanosoma brucei gambiense glycerol kinase complex with PPi (pyrophosphatase reaction)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WXL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 8-18% PEG 400, 0.1M HEPES, 11% 1,6-HEXANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.055 α = 90 b = 120.461 β = 90 c = 154.558 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M 2018-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 2.9 50 99.7 0.04 20.95 3.5 26892
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 2.9 3.07 0.412 2.7 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-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 3WXL 2.9 20 25392 1347 99.55 0.21792 0.21367 0.2198 0.29779 0.2961 RANDOM
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] -0.26 -0.25 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.26 r_dihedral_angle_3_deg 18.208 r_dihedral_angle_4_deg 17.462 r_long_range_B_refined 8.508 r_long_range_B_other 8.507 r_dihedral_angle_1_deg 6.815 r_mcangle_it 5.942 r_mcangle_other 5.942 r_scangle_other 5.901 r_mcbond_it 3.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.26 r_dihedral_angle_3_deg 18.208 r_dihedral_angle_4_deg 17.462 r_long_range_B_refined 8.508 r_long_range_B_other 8.507 r_dihedral_angle_1_deg 6.815 r_mcangle_it 5.942 r_mcangle_other 5.942 r_scangle_other 5.901 r_mcbond_it 3.765 r_mcbond_other 3.764 r_scbond_it 3.685 r_scbond_other 3.685 r_angle_refined_deg 1.344 r_angle_other_deg 0.943 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 7914 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing