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Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with cumarin derivative-17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20-30% PEG 400, 0.1M HEPES, 0.01M
MAGNESIUM SULPHATE, 11% 1,6-HEXANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.03 α = 90 b = 63.205 β = 90.01 c = 154.848 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 PILATUS 2M-F 2016-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1000 Photon Factory BL-1A
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 2.8 50 97.7 0.042 13.2 3.2 56927
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 2.8 2.85 95 0.607 1.35 2.9
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 3WXI 2.85 20 46711 2454 88.72 0.19881 0.19415 0.1976 0.28629 0.2846 RANDOM 55.405
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] -0.22 -0.08 -2.72 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.081 r_dihedral_angle_3_deg 20.063 r_dihedral_angle_4_deg 18.565 r_dihedral_angle_1_deg 8.077 r_long_range_B_refined 5.767 r_long_range_B_other 5.767 r_mcangle_it 3.059 r_mcangle_other 3.059 r_scangle_other 2.834 r_angle_refined_deg 1.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.081 r_dihedral_angle_3_deg 20.063 r_dihedral_angle_4_deg 18.565 r_dihedral_angle_1_deg 8.077 r_long_range_B_refined 5.767 r_long_range_B_other 5.767 r_mcangle_it 3.059 r_mcangle_other 3.059 r_scangle_other 2.834 r_angle_refined_deg 1.865 r_mcbond_it 1.774 r_mcbond_other 1.774 r_scbond_it 1.618 r_scbond_other 1.618 r_angle_other_deg 1.161 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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 15804 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing