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Crystal structure of E. coli YgjK D324N complexed with melibiose
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 2.13 42.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.14 α = 90 b = 138.16 β = 98.37 c = 86.2 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 2010-11-05 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 2.7 50 98 0.116 38773
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 2.7 2.77 97.9 0.343 4.9
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 2.7 40.52 34084 1796 90.91 0.19173 0.18861 0.1913 0.24899 0.2442 RANDOM 25.066
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 37.464 r_dihedral_angle_4_deg 15.364 r_dihedral_angle_3_deg 14.666 r_dihedral_angle_1_deg 6.176 r_angle_other_deg 3.652 r_scangle_it 1.523 r_angle_refined_deg 1.131 r_scbond_it 0.881 r_mcangle_it 0.654 r_mcbond_it 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.464 r_dihedral_angle_4_deg 15.364 r_dihedral_angle_3_deg 14.666 r_dihedral_angle_1_deg 6.176 r_angle_other_deg 3.652 r_scangle_it 1.523 r_angle_refined_deg 1.131 r_scbond_it 0.881 r_mcangle_it 0.654 r_mcbond_it 0.34 r_chiral_restr 0.064 r_mcbond_other 0.046 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined 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 12154 Nucleic Acid Atoms Solvent Atoms 150 Heterogen Atoms 48
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling