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Crystal structure of the quadruple mutant (N23C/C246S/D247E/P249A) of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QKF PDB entry 2QKF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 297 27.7 mg/mL protein mixed 1:1 with reservoir liquor containing
100 mM NaOAc (pH 5.0), 2 mM PEP, 850 microM MnSO4 and 2.0 M NaCl. Immediately prior to data
collection, crystals were harvested and soaked briefly in cryoprotectant solution,
comprising 20% glycerol and the resevoir solution, vapor diffusion, hanging drop, temperature 297K, pH 5.4
Crystal Properties Matthews coefficient Solvent content 2.35 47.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.781 α = 90 b = 85.679 β = 90 c = 163.828 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 110 IMAGE PLATE RIGAKU RAXIS IV++ Osmic blue optic 2007-01-01 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.85 37.96 99.7 0.046 14.1 4.88 98477 98477 31.8
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 1.85 1.92 99.9 0.343 3.4 4.7 9740
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 PDB entry 2QKF 1.85 37.96 98469 98469 4964 99.65 0.207 0.207 0.205 0.211 0.247 0.2463 RANDOM 25.785
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] 0.47 0.3 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.812 r_dihedral_angle_4_deg 21.756 r_dihedral_angle_3_deg 15.417 r_dihedral_angle_1_deg 6.844 r_mcangle_it 3.968 r_scangle_it 3.668 r_mcbond_it 2.873 r_scbond_it 2.443 r_angle_other_deg 1.628 r_mcbond_other 1.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.812 r_dihedral_angle_4_deg 21.756 r_dihedral_angle_3_deg 15.417 r_dihedral_angle_1_deg 6.844 r_mcangle_it 3.968 r_scangle_it 3.668 r_mcbond_it 2.873 r_scbond_it 2.443 r_angle_other_deg 1.628 r_mcbond_other 1.313 r_angle_refined_deg 1.257 r_chiral_restr 0.081 r_gen_planes_refined 0.015 r_bond_refined_d 0.013 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7786 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 27
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction AMoRE phasing