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Crystal structure of glycerol kinase from Entamoeba histolytica complexed with daphnetin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9LYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 293 20 % PEG3350, 0.2 M HCOONa, 50 mM Phosphate buffer (pH 6.8)
Crystal Properties Matthews coefficient Solvent content 2.22 44.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.833 α = 90 b = 81.131 β = 90 c = 204.308 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 2022-05-17 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) Rpim I (All) 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 1.5 50 99.2 0.064 0.066 0.998 14.4 6.8 153933
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 98 0.659 0.71 0.922 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.5 19.91 146265 7582 99.2 0.18017 0.17916 0.188 0.19988 0.206 RANDOM 28.729
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.468 r_dihedral_angle_4_deg 19.93 r_dihedral_angle_3_deg 13.947 r_dihedral_angle_1_deg 6.068 r_long_range_B_refined 4.938 r_long_range_B_other 4.891 r_scangle_other 4.015 r_scbond_it 2.576 r_scbond_other 2.576 r_mcangle_it 2.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.468 r_dihedral_angle_4_deg 19.93 r_dihedral_angle_3_deg 13.947 r_dihedral_angle_1_deg 6.068 r_long_range_B_refined 4.938 r_long_range_B_other 4.891 r_scangle_other 4.015 r_scbond_it 2.576 r_scbond_other 2.576 r_mcangle_it 2.374 r_mcangle_other 2.374 r_mcbond_it 1.652 r_mcbond_other 1.652 r_angle_refined_deg 1.505 r_angle_other_deg 0.966 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 7565 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing