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Crystal structure of Gpb in complex with SUGAR (N-[(2E)-3-(BIPHENYL-4-YL)PROP-2-ENOYL]-BETA-D-GLUCOPYRANOSYLAMINE
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 10mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.87 α = 90 b = 128.87 β = 90 c = 116.65 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 MAR CCD 165 mm 2013-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.04 MAX II I911-2
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 1.99 28.83 94.2 0.094 6.2 2.7 63559 63559 -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 1.99 2.1 71.3 0.451 2.2 2.5 6924
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 28.15 60311 60311 3236 95.41 0.16663 0.16544 0.174 0.18865 0.1967 RANDOM 36.366
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] 0.7 0.7 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.284 r_dihedral_angle_4_deg 19.587 r_dihedral_angle_3_deg 15.432 r_long_range_B_refined 5.936 r_long_range_B_other 5.936 r_dihedral_angle_1_deg 5.89 r_scangle_other 4.159 r_mcangle_it 2.972 r_mcangle_other 2.972 r_scbond_it 2.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.284 r_dihedral_angle_4_deg 19.587 r_dihedral_angle_3_deg 15.432 r_long_range_B_refined 5.936 r_long_range_B_other 5.936 r_dihedral_angle_1_deg 5.89 r_scangle_other 4.159 r_mcangle_it 2.972 r_mcangle_other 2.972 r_scbond_it 2.495 r_scbond_other 2.495 r_mcbond_it 1.89 r_mcbond_other 1.889 r_angle_refined_deg 1.23 r_angle_other_deg 0.793 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6601 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 32
Software Software Software Name Purpose MAR345 data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing