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Crystal structure of Trypanosoma brucei gambiense glycerol kinase phosphorylated at Thr12(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 2.52 51.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.38 α = 90 b = 119.34 β = 90.82 c = 154.73 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 PIXEL DECTRIS EIGER X 16M 2018-11-02 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 2.7 50 95.9 0.05 8.25 1.8 61873
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 2.7 2.86 95.3 0.77 0.8 1.7
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 2.7 19.89 58606 3151 99.1 0.18688 0.18375 0.185 0.2471 0.2484 RANDOM 95.123
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] -0.16 0.02 0.47 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.606 r_dihedral_angle_4_deg 20.014 r_dihedral_angle_3_deg 19.552 r_long_range_B_refined 13.182 r_long_range_B_other 13.181 r_scangle_other 10.18 r_mcangle_it 9.849 r_mcangle_other 9.849 r_dihedral_angle_1_deg 7.378 r_scbond_it 7.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.606 r_dihedral_angle_4_deg 20.014 r_dihedral_angle_3_deg 19.552 r_long_range_B_refined 13.182 r_long_range_B_other 13.181 r_scangle_other 10.18 r_mcangle_it 9.849 r_mcangle_other 9.849 r_dihedral_angle_1_deg 7.378 r_scbond_it 7.041 r_scbond_other 7.041 r_mcbond_it 6.967 r_mcbond_other 6.964 r_angle_refined_deg 1.589 r_angle_other_deg 0.844 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 15836 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing