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Crystal structure of Gpb in complex with S3, SUGAR (N-[(BIPHENYL-4-YLOXY)ACETYL]-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 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.91 α = 90 b = 128.91 β = 90 c = 116.89 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 2013-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.04027 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 2 23.94 79.7 0.073 7.6 2 52566 52566 -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 2.11 83.1 0.347 2.7 1.9 7918
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 23.6 49965 49965 2590 78.58 0.1642 0.16237 0.1625 0.19959 0.2007 RANDOM 31.169
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] 0.75 0.75 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.335 r_dihedral_angle_4_deg 18.756 r_dihedral_angle_3_deg 16.179 r_long_range_B_refined 5.654 r_dihedral_angle_1_deg 5.596 r_mcangle_it 2.548 r_scbond_it 2.245 r_mcbond_it 1.596 r_angle_refined_deg 1.25 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.335 r_dihedral_angle_4_deg 18.756 r_dihedral_angle_3_deg 16.179 r_long_range_B_refined 5.654 r_dihedral_angle_1_deg 5.596 r_mcangle_it 2.548 r_scbond_it 2.245 r_mcbond_it 1.596 r_angle_refined_deg 1.25 r_chiral_restr 0.096 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 295 Heterogen Atoms 28
Software Software Software Name Purpose MAR345 data collection REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing