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Crystal structure of glycerol kinase from Entamoeba histolytica (Ligand-free form)
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 6.8 293 20 % PEG3350, 0.2 M HCOONa, 50 mM Phosphate buffer (pH 6.8)
Crystal Properties Matthews coefficient Solvent content 2.3 46.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.915 α = 90 b = 82.915 β = 90 c = 205.91 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 2019-04-12 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 2 50 99.8 0.064 0.072 0.999 14.4 10.1 64554
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 2.12 0.706 0.835 2.31 9.9
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 2 19.99 64240 3500 99.79 0.18508 0.18212 0.1918 0.23899 0.2428 RANDOM 45.138
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 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.653 r_dihedral_angle_4_deg 20.069 r_dihedral_angle_3_deg 17.315 r_long_range_B_refined 7.879 r_long_range_B_other 7.878 r_dihedral_angle_1_deg 6.881 r_scangle_other 6.684 r_scbond_it 4.607 r_scbond_other 4.607 r_mcangle_it 4.567
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.653 r_dihedral_angle_4_deg 20.069 r_dihedral_angle_3_deg 17.315 r_long_range_B_refined 7.879 r_long_range_B_other 7.878 r_dihedral_angle_1_deg 6.881 r_scangle_other 6.684 r_scbond_it 4.607 r_scbond_other 4.607 r_mcangle_it 4.567 r_mcangle_other 4.567 r_mcbond_it 3.545 r_mcbond_other 3.544 r_angle_refined_deg 1.842 r_angle_other_deg 1.102 r_chiral_restr 0.134 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 7560 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing