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Crystal Structure of Inhibitor-bound Galactokinase
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 6.8 286 Seeding into drops containing GALK protein at 8 mg/ml, 2.3M Na/K pH6.8
Crystal Properties Matthews coefficient Solvent content 3.44 64.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.216 α = 90 b = 129.216 β = 90 c = 240.789 γ = 120
Symmetry Space Group P 61 2 2
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 PSI PILATUS 6M 2015-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.1271 SSRL BL7-1
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 2.2 38.61 99.8 0.107 0.109 0.024 0.999 21.3 21 61072
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 2.2 2.25 97.2 0.893 0.928 0.247 0.842 13.5
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 2.2 38.61 58715 2268 99.74 0.1775 0.1761 0.1759 0.2146 0.2144 RANDOM 45.503
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] -1.18 -0.59 -1.18 3.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.963 r_dihedral_angle_4_deg 21.449 r_dihedral_angle_3_deg 16.921 r_dihedral_angle_1_deg 7.6 r_angle_refined_deg 1.759 r_angle_other_deg 0.807 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.963 r_dihedral_angle_4_deg 21.449 r_dihedral_angle_3_deg 16.921 r_dihedral_angle_1_deg 7.6 r_angle_refined_deg 1.759 r_angle_other_deg 0.807 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5900 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 232
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction