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The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-xylose bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G1A PDB 1G1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 35% PEG 4000, 0.1M Citric acid pH 5.4, 0.3M ammonium sulphate and 3% 1,6-hexanediol,
VAPOR DIFFUSION, HANGING DROP at 293K
Crystal Properties Matthews coefficient Solvent content 3.61 65.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.449 α = 90 b = 97.182 β = 90 c = 185.471 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 morrors 2001-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 0.870 SRS PX9.6
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 1.8 91.3 97 0.094 0.079 6.9 3.3 102080 91826 15.82
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 1.8 1.9 85.1 0.364 0.291 2.5 2.3 12822
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB 1G1A 1.8 91.29 102080 91826 10151 96.83 0.14795 0.14525 0.17238 RANDOM 6.427
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] 0.03 0.32 -0.35
RMS Deviations Key Refinement Restraint Deviation p_scangle_it 4.132 p_scbond_it 2.565 p_angle_d 1.771 p_angle_deg 1.771 p_mcangle_it 1.472 p_mcbond_it 0.802 p_bond_d 0.019
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5478 Nucleic Acid Atoms Solvent Atoms 804 Heterogen Atoms 149
Software Software Software Name Purpose AMoRE phasing REFMAC refinement MOSFLM data reduction CCP4 data scaling