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Structure of human galactokinase in complex with galactose and 2'-(benzo[d]oxazol-2-ylamino)-7',8'-dihydro-1'H-spiro[cyclopentane-1,4'-quinazolin]-5'(6'H)-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WUU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Morpheus condition:
Buffer system 1:
0.1 M pH 6.5, Imidazole; MES monohydrate (acid)
Amino acids:
0.02M L-Na-Glutamate; 0.02M Alanine (racemic); 0.02M Glycine; 0.02M Lysine HCl (racemic); 0.02M Serine (racemic)
Precipitant Mix 1:
20% v/v PEG 500 MME; 10 % w/v PEG 20000
Crystal Properties Matthews coefficient Solvent content 2.42 49.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.872 α = 90 b = 97.204 β = 98.51 c = 144.812 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 6M-F 2018-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.439 98.79 99.3 0.325 0.126 6 6.6 121943 41.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.48 96.9 3.561 1.375 1 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1WUU 2.439 98.787 1.34 121627 5980 99.06 0.2122 0.2097 0.2088 0.2619 0.26 58.6014
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22210 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 271
Software Software Software Name Purpose xia2 data scaling PHENIX refinement PDB_EXTRACT data extraction Aimless data reduction PHASER phasing