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Crystal structure of Gpb in complex with SUGAR (N-[4-(5,6,7,8-TETRAHYDRONAPHTHALEN-2-YL)BUTANOYL]-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 52.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.9 α = 90 b = 128.9 β = 90 c = 116.54 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 2013-02-21 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 1.9 23.94 98.1 0.055 13.2 3.4 75897 75897 -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 1.9 2 97.1 0.365 3.2 3.4 10836
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 1.9 23.71 72040 72040 3821 97.78 0.16265 0.16131 0.1709 0.1885 0.1925 RANDOM 31.341
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] 0.71 0.71 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.316 r_dihedral_angle_4_deg 18.972 r_dihedral_angle_3_deg 15.05 r_dihedral_angle_1_deg 5.812 r_long_range_B_refined 5.182 r_long_range_B_other 5.182 r_scangle_other 3.577 r_mcangle_it 2.461 r_mcangle_other 2.461 r_scbond_it 2.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.316 r_dihedral_angle_4_deg 18.972 r_dihedral_angle_3_deg 15.05 r_dihedral_angle_1_deg 5.812 r_long_range_B_refined 5.182 r_long_range_B_other 5.182 r_scangle_other 3.577 r_mcangle_it 2.461 r_mcangle_other 2.461 r_scbond_it 2.119 r_scbond_other 2.119 r_mcbond_it 1.52 r_mcbond_other 1.52 r_angle_refined_deg 1.186 r_angle_other_deg 0.804 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 6601 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 27
Software Software Software Name Purpose MAR345 data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing