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Crystal structure of the triple mutant (N23C/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 5 297 21.0 mg/mL protein mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 5.0), 2 mM PEP, 200 microM MnSO4 and 2.0 M NaCl. Immediately prior to data collection, crystal were harvested and soaked briefly in cryoprotectant solution, comprising 20% glycerol and 100 mM NaOAc (pH 5.0) and 2.0 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.4 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.74 α = 90 b = 86.197 β = 90 c = 163.891 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 2006-11-15 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 1.8 33.95 99.5 0.065 9 4.15 108582 108582 32.4
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 1.8 1.86 100 0.472 2.3 4.09 10737
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 1.9 33.94 92429 92429 4644 99.42 0.218 0.218 0.216 0.2172 0.257 0.2595 RANDOM 27.845
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] 0.6 0.25 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.127 r_dihedral_angle_4_deg 19.389 r_dihedral_angle_3_deg 16.356 r_dihedral_angle_1_deg 6.743 r_scangle_it 5.102 r_scbond_it 3.265 r_mcangle_it 2.167 r_mcbond_it 1.306 r_angle_refined_deg 1.075 r_angle_other_deg 0.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.127 r_dihedral_angle_4_deg 19.389 r_dihedral_angle_3_deg 16.356 r_dihedral_angle_1_deg 6.743 r_scangle_it 5.102 r_scbond_it 3.265 r_mcangle_it 2.167 r_mcbond_it 1.306 r_angle_refined_deg 1.075 r_angle_other_deg 0.946 r_mcbond_other 0.502 r_chiral_restr 0.139 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7886 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 14
Software Software Software Name Purpose d*TREK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction