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Escherichia coli K12 YgjK complexed with mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 293 20% PEG 8000, 0.6M magnesium chloride, 100mM Tris-HCl buffer, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.467 α = 90 b = 137.844 β = 98.07 c = 86.524 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 4 2007-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A
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 1.5 50 96.6 0.063 222770
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 1.5 1.55 98.8 0.388 3.93
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 2DS3 1.5 46.03 200354 22199 96.47 0.15666 0.15406 0.1628 0.18033 0.1869 RANDOM 15.792
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 36.052 r_dihedral_angle_4_deg 16.437 r_dihedral_angle_3_deg 11.549 r_dihedral_angle_1_deg 6.069 r_scangle_it 2.909 r_scbond_it 1.811 r_angle_refined_deg 1.275 r_mcangle_it 1.114 r_angle_other_deg 0.756 r_mcbond_it 0.606
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.052 r_dihedral_angle_4_deg 16.437 r_dihedral_angle_3_deg 11.549 r_dihedral_angle_1_deg 6.069 r_scangle_it 2.909 r_scbond_it 1.811 r_angle_refined_deg 1.275 r_mcangle_it 1.114 r_angle_other_deg 0.756 r_mcbond_it 0.606 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_mcbond_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 1656 Heterogen Atoms 88
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling