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Activated state yGsy2p in complex with UDP-2-fluoro-2-deoxy-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KQM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 25 - 30 % Peg 300, 0.1 M Bis-Tris pH 6.1-6.4, 25 mM G-6-P, 10 mM UDP-FDG
Crystal Properties Matthews coefficient Solvent content 3.12 64.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.516 α = 90 b = 204.705 β = 90 c = 206.514 γ = 90
Symmetry Space Group I 2 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 PIXEL DECTRIS PILATUS3 S 6M 2015-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.979 APS 23-ID-D
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 2.73 145.38 99.4 0.055 0.046 0.999 11.97 4.21 102119
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 4KQM 2.73 145.38 102019 5465 99.49 0.20012 0.19876 0.2005 0.22449 0.2227 RANDOM 80.761
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] -2.61 3.75 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.353 r_dihedral_angle_4_deg 18.685 r_dihedral_angle_3_deg 14.924 r_dihedral_angle_1_deg 5.872 r_long_range_B_refined 4.942 r_long_range_B_other 4.942 r_mcangle_it 2.82 r_mcangle_other 2.82 r_scangle_other 2.787 r_mcbond_it 1.617
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.353 r_dihedral_angle_4_deg 18.685 r_dihedral_angle_3_deg 14.924 r_dihedral_angle_1_deg 5.872 r_long_range_B_refined 4.942 r_long_range_B_other 4.942 r_mcangle_it 2.82 r_mcangle_other 2.82 r_scangle_other 2.787 r_mcbond_it 1.617 r_mcbond_other 1.616 r_scbond_it 1.583 r_scbond_other 1.583 r_angle_refined_deg 1.384 r_angle_other_deg 0.948 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 20321 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing