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Crystal structure of F114A 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. Immediately prior to data collection, crystals were harvested and soaked briefly in cryoprotectant solution, comprising 20% glycerol and the reservoir solution, Vapor diffusion, hanging drop, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.33 47.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.355 α = 90 b = 85.473 β = 90 c = 163.057 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++ 2007-03-05 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 1.9 39.95 97.8 0.065 8.8 4.7 88194
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 1.9 1.97 87 0.601 1.2 4.37 7731
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 1.9 39.95 87105 4369 97.2 0.2305 0.2286 0.2315 0.2669 0.2661 RANDOM 46.8224
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] 1.01 0.6 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.222 r_dihedral_angle_4_deg 17.637 r_dihedral_angle_3_deg 15.393 r_dihedral_angle_1_deg 5.588 r_mcangle_it 3.772 r_mcbond_it 2.727 r_mcbond_other 2.727 r_angle_refined_deg 1.757 r_angle_other_deg 1.583 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.222 r_dihedral_angle_4_deg 17.637 r_dihedral_angle_3_deg 15.393 r_dihedral_angle_1_deg 5.588 r_mcangle_it 3.772 r_mcbond_it 2.727 r_mcbond_other 2.727 r_angle_refined_deg 1.757 r_angle_other_deg 1.583 r_chiral_restr 0.093 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7732 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 3
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection