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Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N-(pyrimidin-2-yl)acetamide
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 0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of - sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate and sodium oxamate).
Crystal Properties Matthews coefficient Solvent content 2.88 57.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.21 α = 90 b = 114.299 β = 100.54 c = 120.807 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 2018-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.07 114.3 100 0.144 0.171 0.092 0.99 5.9 3.4 118894
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.12 99.9 1.329 1.6 0.881 0.49 3.2
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 1WUU 2.3 82.49 82481 4253 99.84 0.2163 0.2142 0.2173 0.2563 0.2565 RANDOM 43.168
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] -2.32 -0.17 3.66 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.305 r_dihedral_angle_4_deg 18.926 r_dihedral_angle_3_deg 16.857 r_dihedral_angle_1_deg 8.187 r_angle_refined_deg 1.857 r_angle_other_deg 1.415 r_chiral_restr 0.078 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.305 r_dihedral_angle_4_deg 18.926 r_dihedral_angle_3_deg 16.857 r_dihedral_angle_1_deg 8.187 r_angle_refined_deg 1.857 r_angle_other_deg 1.415 r_chiral_restr 0.078 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10871 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 130
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing