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Crystal structure of R117K mutant 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 4.6 297 20 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 0.6-3.0 M NaCl, cryoprotectant 20% glycerol and reservoir solution, Vapor diffusion, hanging drop, temperature 297K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.468 α = 90 b = 85.37 β = 90 c = 163.023 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 120 IMAGE PLATE RIGAKU RAXIS IV++ 2005-12-02 M 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 1.75 39.93 98.8 0.041 14.1 4.07 113642
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 1.75 1.81 93 0.325 2.7 2.39 10577
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2QKF 1.75 39.55 113637 5687 98.5 0.1979 0.1965 0.2029 0.2263 0.2291 RANDOM 35.9257
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] 0.54 0.18 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.83 r_dihedral_angle_4_deg 18.805 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_1_deg 5.7 r_mcangle_it 3.555 r_mcbond_it 2.487 r_mcbond_other 2.485 r_angle_refined_deg 1.797 r_angle_other_deg 1.698 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.83 r_dihedral_angle_4_deg 18.805 r_dihedral_angle_3_deg 14.674 r_dihedral_angle_1_deg 5.7 r_mcangle_it 3.555 r_mcbond_it 2.487 r_mcbond_other 2.485 r_angle_refined_deg 1.797 r_angle_other_deg 1.698 r_chiral_restr 0.105 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.01 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7874 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 4
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection