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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 64.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.407 α = 90 b = 129.407 β = 90 c = 240.548 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) 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 30 99.3 0.175 0.177 0.023 7.2 42.7 60586
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 95.3 0.375 0.611 16.5
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 30 58502 2000 99.19 0.1601 0.1579 0.1579 0.2255 0.2256 RANDOM 54.983
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] -1.53 -0.76 -1.53 4.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.739 r_dihedral_angle_4_deg 18.984 r_dihedral_angle_3_deg 17.197 r_dihedral_angle_1_deg 7.503 r_rigid_bond_restr 3.958 r_angle_refined_deg 1.741 r_angle_other_deg 1.363 r_chiral_restr 0.223 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.739 r_dihedral_angle_4_deg 18.984 r_dihedral_angle_3_deg 17.197 r_dihedral_angle_1_deg 7.503 r_rigid_bond_restr 3.958 r_angle_refined_deg 1.741 r_angle_other_deg 1.363 r_chiral_restr 0.223 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 242 Heterogen Atoms 146
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHENIX phasing