2QKF

Crystal structure of 3-deoxy-d-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.6295CRYSTALLISATION CONDITIONS: 18.6 MG/ML PROTEIN MIXED 1:1 WITH RESERVOIR LIQUOR CONTAINING 100 MM SODIUM ACETATE PH 4.60, 200 MICROMOLAR PEP, 0.6, 1.6 MOLAR SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3249

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.515α = 90
b = 85.295β = 90
c = 162.686γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IVOSMIC BLUE MIRRORS2005-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7540970.04313.43.9511133331.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8178.20.3682.74.16

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1D9E1.75401113331057445588970.1970.1960.235RANDOM30.27
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]
0.910.2-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.994
r_dihedral_angle_4_deg17.825
r_dihedral_angle_3_deg13.796
r_dihedral_angle_1_deg5.619
r_mcangle_it2.874
r_mcbond_it1.869
r_scangle_it1.683
r_angle_refined_deg1.306
r_scbond_it1.041
r_angle_other_deg0.817
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.994
r_dihedral_angle_4_deg17.825
r_dihedral_angle_3_deg13.796
r_dihedral_angle_1_deg5.619
r_mcangle_it2.874
r_mcbond_it1.869
r_scangle_it1.683
r_angle_refined_deg1.306
r_scbond_it1.041
r_angle_other_deg0.817
r_mcbond_other0.665
r_symmetry_vdw_refined0.242
r_nbd_other0.222
r_symmetry_vdw_other0.215
r_nbd_refined0.213
r_symmetry_hbond_refined0.206
r_xyhbond_nbd_refined0.171
r_nbtor_refined0.17
r_metal_ion_refined0.143
r_nbtor_other0.112
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7748
Nucleic Acid Atoms
Solvent Atoms528
Heterogen Atoms30

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
MOLREPphasing