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THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TDP-L-RHAMNOSE COMPLEX.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G1L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 292 10 % (w/v) PEG 6000,
0.2 M Li-sulfate,
0.1 M Na-citrate pH 4.0;
protein incubated with 10 mM dTDP-L-rhamnose, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.55 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.087 α = 90 b = 138.557 β = 90 c = 139.676 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 IMAGE PLATE RIGAKU RAXIS 2000-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 49.9 94.2 0.12 6.8 7.2 36311 37.11
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) 2.8 2.84 70.8 0.266 2.9 5.7
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 THROUGHOUT 1G1L 2.7 100 34462 1815 93.8 0.205 0.204 0.2129 0.23 0.2344 RANDOM 12.78
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] 1.07 0.01 -1.08
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 1.772 p_scbond_it 1.097 p_mcangle_it 0.847 p_mcbond_it 0.48 p_chiral_restr 0.102 p_bond_d 0.014 p_plane_restr 0.006 p_angle_d p_angle_deg p_planar_d
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 1.772 p_scbond_it 1.097 p_mcangle_it 0.847 p_mcbond_it 0.48 p_chiral_restr 0.102 p_bond_d 0.014 p_plane_restr 0.006 p_angle_d p_angle_deg p_planar_d p_hb_or_metal_coord p_singtor_nbd p_multtor_nbd p_xhyhbond_nbd p_xyhbond_nbd p_planar_tor p_staggered_tor p_orthonormal_tor p_transverse_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9148 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 305
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction CCP4 data scaling