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Crystal structure of a mutant (K57A) 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 2.38 48.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.428 α = 90 b = 86.183 β = 90 c = 163.312 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++ 2010-03-22 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 1.95 34.59 98 0.079 8.6 5.15 83787 83787
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 1.95 2.02 100 0.394 3 5.16 8432
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 1.95 33.84 83643 83643 4210 97.91 0.2071 0.2071 0.2048 0.1999 0.2521 0.2467 RANDOM 37.0264
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] -1.12 0.94 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.675 r_dihedral_angle_4_deg 20.573 r_dihedral_angle_3_deg 16.718 r_dihedral_angle_1_deg 6.623 r_scangle_it 6.365 r_scbond_it 3.874 r_mcangle_it 2.413 r_mcbond_it 1.397 r_angle_refined_deg 1.09 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.675 r_dihedral_angle_4_deg 20.573 r_dihedral_angle_3_deg 16.718 r_dihedral_angle_1_deg 6.623 r_scangle_it 6.365 r_scbond_it 3.874 r_mcangle_it 2.413 r_mcbond_it 1.397 r_angle_refined_deg 1.09 r_chiral_restr 0.092 r_gen_planes_refined 0.012 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7688 Nucleic Acid Atoms Solvent Atoms 737 Heterogen Atoms 10
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction