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Crystal structure of a double mutant [A58P, DEL(N59)] 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 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.82 α = 90 b = 85.15 β = 90 c = 163.78 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 100 CCD ADSC QUANTUM 315r 2010-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 54.593 99.7 0.119 10.2 4.7 32102 32102
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.85 99.5 0.503 0.503 0.564 0.251 1.5 4.8 4620
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2QKF 2.7 47.89 32051 32051 1562 99.59 0.2143 0.2143 0.2112 0.2749 0.253 RANDOM 34.3241
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 0.41 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_4_deg 17.407 r_dihedral_angle_3_deg 17.072 r_dihedral_angle_1_deg 5.082 r_scangle_it 2.645 r_scbond_it 1.424 r_mcangle_it 1.251 r_angle_refined_deg 1.115 r_mcbond_it 0.655 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.305 r_dihedral_angle_4_deg 17.407 r_dihedral_angle_3_deg 17.072 r_dihedral_angle_1_deg 5.082 r_scangle_it 2.645 r_scbond_it 1.424 r_mcangle_it 1.251 r_angle_refined_deg 1.115 r_mcbond_it 0.655 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7662 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection