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The high resolution structures of RmlC from Streptococcus suis in complex with dTDP-D-xylose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NYW PDB entry 1NYW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 298 0.1 M Tris, 4 mM NiCl2,10 mM dTDP-D-xylose, 35% PEG 2000, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.88 33.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.85 α = 90 b = 140.866 β = 92.72 c = 53.699 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 120 CCD ADSC QUANTUM 4 2001-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
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 50.79 91.8 0.126 0.117 3.8 5.3 63995 63969 2.96 3.1 21.38
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) 1.8 1.81 43.3 0.112 0.085 8.1 2.1 500
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 1NYW 1.8 70.71 2.574 87974 60716 3217 91.8 0.16698 0.16445 0.1924 0.21562 0.2329 RANDOM 17.913
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] -0.44 -0.03 -0.02 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.41 r_sphericity_free 2.886 r_scangle_it 2.882 r_scbond_it 1.847 r_angle_refined_deg 1.577 r_mcangle_it 1.294 r_rigid_bond_restr 1.119 r_sphericity_bonded 1.069 r_angle_other_deg 0.911 r_mcbond_it 0.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.41 r_sphericity_free 2.886 r_scangle_it 2.882 r_scbond_it 1.847 r_angle_refined_deg 1.577 r_mcangle_it 1.294 r_rigid_bond_restr 1.119 r_sphericity_bonded 1.069 r_angle_other_deg 0.911 r_mcbond_it 0.747 r_symmetry_hbond_refined 0.35 r_symmetry_vdw_refined 0.289 r_symmetry_vdw_other 0.271 r_nbd_other 0.256 r_nbd_refined 0.196 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.103 r_nbtor_other 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6304 Nucleic Acid Atoms Solvent Atoms 874 Heterogen Atoms 138
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling