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Crystal structure of SdgB (complexed with UDP, GlcNAc, and Glycosylated peptide)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287 20 mM CaCl2, 85 mM tri-sodium citrate at pH 5.6, 25.5% (w/v) PEG 4,000, and 15% (w/v) glycerol for the SdgB crystal soaked with the 2.66 mM 9mer SD-repeat peptide and 9.60 mM UDP-GlcNAc
Crystal Properties Matthews coefficient Solvent content 3.65 66.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.201 α = 90 b = 130.568 β = 90 c = 189.854 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 4M 2015-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1000 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.5 50 96.7 0.934 12.9 5.4 60708
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 0.776
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 7EC1 2.5 47.05 57606 3041 93.1 0.193 0.191 0.2017 0.24 0.2451 RANDOM 38.96
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] -1.77 4.83 -3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.767 r_dihedral_angle_4_deg 19.826 r_dihedral_angle_3_deg 17.141 r_dihedral_angle_1_deg 7.417 r_angle_refined_deg 1.707 r_angle_other_deg 1.247 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.767 r_dihedral_angle_4_deg 19.826 r_dihedral_angle_3_deg 17.141 r_dihedral_angle_1_deg 7.417 r_angle_refined_deg 1.707 r_angle_other_deg 1.247 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8433 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing