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Crystal structure of F139G 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 solution, comprising 20% glycerol and reservoir solution, Vapor diffusion, hanging drop, temperature 297K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.997 α = 90 b = 85.924 β = 90 c = 163.37 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++ 2010-02-05 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 2.1 38.06 92 0.08 7.2 3.12 62633
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 2.1 2.18 99.9 0.395 2.3 3.08 6692
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 2.1 37.09 62592 3143 91.78 0.2186 0.217 0.223 0.2499 0.2572 RANDOM 40.4761
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] 0.09 1.42 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.875 r_dihedral_angle_4_deg 18.016 r_dihedral_angle_3_deg 15.753 r_dihedral_angle_1_deg 5.919 r_mcangle_it 4.041 r_mcbond_it 2.807 r_mcbond_other 2.807 r_angle_refined_deg 1.709 r_angle_other_deg 1.507 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.875 r_dihedral_angle_4_deg 18.016 r_dihedral_angle_3_deg 15.753 r_dihedral_angle_1_deg 5.919 r_mcangle_it 4.041 r_mcbond_it 2.807 r_mcbond_other 2.807 r_angle_refined_deg 1.709 r_angle_other_deg 1.507 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_bond_other_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7759 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 2
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection