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Activated state yGsy2p in complex with UDP-galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NB0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 25 - 30 % Peg 300, 0.1 M Bis-Tris pH 6.1-6.4, 25 mM G-6-P, 10 mM UDP-Gal
Crystal Properties Matthews coefficient Solvent content 3.13 65.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.665 α = 90 b = 206.446 β = 90 c = 205.099 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 100 PIXEL DECTRIS PILATUS3 S 6M 2016-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.979 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.26 145.5 98.3 15.3 4.1 63020
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 3NB0 3.26 145.5 59712 3255 98.25 0.1877 0.18534 0.1877 0.23025 0.2258 RANDOM 105.568
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] -0.28 -4.15 4.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.227 r_dihedral_angle_4_deg 15.835 r_dihedral_angle_3_deg 15.61 r_dihedral_angle_1_deg 6.298 r_long_range_B_refined 5.806 r_long_range_B_other 5.806 r_mcangle_it 3.456 r_mcangle_other 3.456 r_scangle_other 3.281 r_mcbond_it 1.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.227 r_dihedral_angle_4_deg 15.835 r_dihedral_angle_3_deg 15.61 r_dihedral_angle_1_deg 6.298 r_long_range_B_refined 5.806 r_long_range_B_other 5.806 r_mcangle_it 3.456 r_mcangle_other 3.456 r_scangle_other 3.281 r_mcbond_it 1.988 r_mcbond_other 1.987 r_scbond_it 1.849 r_scbond_other 1.849 r_angle_refined_deg 1.38 r_angle_other_deg 0.95 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 20295 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing