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Crystal structure of SdgB (complexed with peptides)
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 0.2 M MgCl2, 0.1 M Tris-HCl (pH 8.5), and 25% (w/v) polyethylene glycol (PEG) 3,350 incubated with the 2.45 mM 3-mer SD-repeat peptide and 6.14 mM UDP-GlcNAc
Crystal Properties Matthews coefficient Solvent content 2.39 48.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.15 α = 90 b = 206.172 β = 105.32 c = 66.4 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 270 2014-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
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 1.9 30 99.3 0.992 26 4.1 87189
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 1.9 1.93 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7EC1 1.9 29.04 82563 4391 99.24 0.231 0.2294 0.2609 0.2597 RANDOM 38.075
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] -1.05 -0.64 0.85 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.436 r_dihedral_angle_4_deg 19.763 r_dihedral_angle_3_deg 14.564 r_dihedral_angle_1_deg 7.025 r_angle_refined_deg 1.546 r_angle_other_deg 1.285 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.436 r_dihedral_angle_4_deg 19.763 r_dihedral_angle_3_deg 14.564 r_dihedral_angle_1_deg 7.025 r_angle_refined_deg 1.546 r_angle_other_deg 1.285 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8208 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing