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Structure of the YicI thiosugar Michaelis complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XSI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 10 mg/ml protein, 100mM Na Acetate, pH 6.5, 2M Ammonium Sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.84 56.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.317 α = 90 b = 175.841 β = 90 c = 210.742 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 CCD ADSC QUANTUM 4 2005-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.95516 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 28.64 86.5 0.097 0.097 7.3 3.4 375658 375731 16.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 88.9 0.433 0.433 1.7 3 55875
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1XSI 1.95 28.64 375658 375658 18828 86.36 0.182 0.182 0.18 0.1883 0.225 0.2306 RANDOM 18.288
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] -0.29 -1.31 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.157 r_dihedral_angle_4_deg 19.024 r_dihedral_angle_3_deg 16.421 r_dihedral_angle_1_deg 7.565 r_scangle_it 3.068 r_scbond_it 2.163 r_angle_refined_deg 1.748 r_mcangle_it 1.33 r_mcbond_it 1.117 r_angle_other_deg 0.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.157 r_dihedral_angle_4_deg 19.024 r_dihedral_angle_3_deg 16.421 r_dihedral_angle_1_deg 7.565 r_scangle_it 3.068 r_scbond_it 2.163 r_angle_refined_deg 1.748 r_mcangle_it 1.33 r_mcbond_it 1.117 r_angle_other_deg 0.963 r_symmetry_vdw_other 0.282 r_mcbond_other 0.223 r_nbd_refined 0.205 r_nbd_other 0.199 r_symmetry_vdw_refined 0.199 r_nbtor_refined 0.185 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.125 r_nbtor_other 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37392 Nucleic Acid Atoms Solvent Atoms 2003 Heterogen Atoms 404
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling CNS phasing