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CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI GAMBIENSE GLYCEROL KINASE COMPLEX WITH ADP and G3P
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J9V
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, PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.563 α = 90 b = 121.741 β = 90 c = 154.278 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 2018-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.4 50 99.8 0.054 0.999 18.5 13.6 45369
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.55 99.1 0.719 0.842 2 12.2
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 6J9V 2.4 19.86 44323 2326 99.75 0.19518 0.19226 0.2075 0.24982 0.257 RANDOM 73.455
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] 0.07 -0.04 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.494 r_dihedral_angle_3_deg 18.103 r_dihedral_angle_4_deg 18.091 r_long_range_B_refined 9.947 r_long_range_B_other 9.947 r_scangle_other 7.626 r_dihedral_angle_1_deg 7.021 r_mcangle_it 6.29 r_mcangle_other 6.289 r_scbond_it 5.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.494 r_dihedral_angle_3_deg 18.103 r_dihedral_angle_4_deg 18.091 r_long_range_B_refined 9.947 r_long_range_B_other 9.947 r_scangle_other 7.626 r_dihedral_angle_1_deg 7.021 r_mcangle_it 6.29 r_mcangle_other 6.289 r_scbond_it 5.129 r_scbond_other 5.129 r_mcbond_it 4.515 r_mcbond_other 4.515 r_angle_refined_deg 1.565 r_angle_other_deg 1.002 r_chiral_restr 0.086 r_bond_refined_d 0.011 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 7912 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing