4JTI

Crystal structure of F114R/R117Q/F139G mutant of 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QKFPDB entry 2QKF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629720 mg/mL protein (in 10 mM BTP pH 7.5) mixed 1:1 with reservoir liquor containing 100 mM NaOAc (pH 4.6) and 1.6 M NaCl, cryoprotectant 20% glycerol and the reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.3347.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.67α = 90
b = 85.2β = 90
c = 162.85γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95369Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.7540.8351000.08813.67.2115042115042
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.841000.4190.4191.87.316641

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2QKF1.7540.82114951575199.930.16040.1590.1884RANDOM28.5823
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]
0.80.6-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.595
r_dihedral_angle_4_deg23.95
r_dihedral_angle_3_deg13.525
r_dihedral_angle_1_deg5.827
r_mcangle_it3.316
r_mcbond_it2.293
r_mcbond_other2.293
r_angle_refined_deg1.959
r_angle_other_deg1.855
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.595
r_dihedral_angle_4_deg23.95
r_dihedral_angle_3_deg13.525
r_dihedral_angle_1_deg5.827
r_mcangle_it3.316
r_mcbond_it2.293
r_mcbond_other2.293
r_angle_refined_deg1.959
r_angle_other_deg1.855
r_chiral_restr0.113
r_bond_refined_d0.021
r_bond_other_d0.012
r_gen_planes_refined0.012
r_gen_planes_other0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7863
Nucleic Acid Atoms
Solvent Atoms716
Heterogen Atoms5

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection