3QPY

Crystal structure of a mutant (K57A) 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 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 coefficientSolvent content
2.3848.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.428α = 90
b = 86.183β = 90
c = 163.312γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV++2010-03-22SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
11.9534.59980.0798.65.158378783787
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)
11.952.021000.39435.168432

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2QKF1.9533.848364383643421097.910.20710.20710.20480.2521RANDOM37.0264
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]
-1.120.940.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.675
r_dihedral_angle_4_deg20.573
r_dihedral_angle_3_deg16.718
r_dihedral_angle_1_deg6.623
r_scangle_it6.365
r_scbond_it3.874
r_mcangle_it2.413
r_mcbond_it1.397
r_angle_refined_deg1.09
r_chiral_restr0.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.675
r_dihedral_angle_4_deg20.573
r_dihedral_angle_3_deg16.718
r_dihedral_angle_1_deg6.623
r_scangle_it6.365
r_scbond_it3.874
r_mcangle_it2.413
r_mcbond_it1.397
r_angle_refined_deg1.09
r_chiral_restr0.092
r_gen_planes_refined0.012
r_bond_refined_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7688
Nucleic Acid Atoms
Solvent Atoms737
Heterogen Atoms10

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction