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Crystal structure of glycerol kinase from Entamoeba histolytica complexed with GK-butyl.
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 2.27 45.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.865 α = 90 b = 204.26 β = 90 c = 82.63 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 2023-11-18 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 1.89 50 99.1 0.081 0.091 0.999 13.5 6.8 78241
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 1.89 2.01 1.156 0.782 2.1
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 1.89 19.95 74075 4020 99.12 0.19492 0.19325 0.2019 0.22468 0.2287 RANDOM 40.631
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.761 r_dihedral_angle_4_deg 19.557 r_dihedral_angle_3_deg 15.299 r_dihedral_angle_1_deg 6.306 r_long_range_B_other 5.853 r_long_range_B_refined 5.851 r_scangle_other 4.618 r_mcangle_it 3.094 r_mcangle_other 3.094 r_scbond_it 2.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.761 r_dihedral_angle_4_deg 19.557 r_dihedral_angle_3_deg 15.299 r_dihedral_angle_1_deg 6.306 r_long_range_B_other 5.853 r_long_range_B_refined 5.851 r_scangle_other 4.618 r_mcangle_it 3.094 r_mcangle_other 3.094 r_scbond_it 2.958 r_scbond_other 2.946 r_mcbond_it 2.177 r_mcbond_other 2.176 r_angle_refined_deg 1.449 r_angle_other_deg 0.962 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 7555 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing