☰ Navigation Tabs
Crystal structure of Gpb in complex with SUGAR (N-{(2E)-3-[4-(PROPAN-2-YL)PHENYL]PROP-2-ENOYL}-BETA-D-GLUCOPYRANOSYLAMINE) (S6)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SYM pdb entry 3SYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 289 10 mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.59 52.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.74 α = 90 b = 128.74 β = 90 c = 116.71 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD AGILENT ATLAS CCD 2013-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.5419
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.45 18.23 91.4 0.099 6.3 2.2 33056 33056 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.58 95.6 0.531 1.8 2.2 4997
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT pdb entry 3SYM 2.45 18.14 31316 31316 1646 89.96 0.18899 0.18663 0.1923 0.23354 0.2309 RANDOM 36.423
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] 0.72 0.72 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.868 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 15.392 r_dihedral_angle_1_deg 5.393 r_angle_refined_deg 0.981 r_angle_other_deg 0.74 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.868 r_dihedral_angle_4_deg 17.8 r_dihedral_angle_3_deg 15.392 r_dihedral_angle_1_deg 5.393 r_angle_refined_deg 0.981 r_angle_other_deg 0.74 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6577 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 25
Software Software Software Name Purpose CrysalisPro data collection REFMAC refinement CrysalisPro data reduction SCALA data scaling REFMAC phasing