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Crystal structure of E. coli YgjK E727A complexed with 2-O-alpha-D-glucopyranosyl-alpha-D-galactopyranose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C68
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 20% PEG 8000, 0.6M magnesium chloride, 100mM Tris-HCl buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 1.93 36.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.884 α = 90 b = 138.136 β = 99.03 c = 82.547 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 210r 2011-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 100 0.103 86824
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.06 100 0.413 4.1
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 3C68 2 31.88 82438 4347 99.39 0.17635 0.17376 0.1806 0.22594 0.2322 RANDOM 18.911
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.545 r_dihedral_angle_4_deg 14.742 r_dihedral_angle_3_deg 13.356 r_dihedral_angle_1_deg 6.081 r_scangle_it 2.431 r_scbond_it 1.501 r_angle_refined_deg 1.198 r_mcangle_it 0.949 r_angle_other_deg 0.839 r_mcbond_it 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.545 r_dihedral_angle_4_deg 14.742 r_dihedral_angle_3_deg 13.356 r_dihedral_angle_1_deg 6.081 r_scangle_it 2.431 r_scbond_it 1.501 r_angle_refined_deg 1.198 r_mcangle_it 0.949 r_angle_other_deg 0.839 r_mcbond_it 0.51 r_mcbond_other 0.108 r_chiral_restr 0.072 r_bond_refined_d 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12136 Nucleic Acid Atoms Solvent Atoms 869 Heterogen Atoms 55
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling