1O60

Crystal structure of KDO-8-phosphate synthase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop vapor diffusion7.5293
Crystal Properties
Matthews coefficientSolvent content
2.0840.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.965α = 90
b = 92.893β = 116.82
c = 82.301γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARRESEARCHSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID0.9796APS32-ID

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
11.839.2297.70.05815.53.89569395693
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)
11.81.997.70.2345.53.8

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONSe-Met SAD phasing1.839.229568995400.2070.24224.423
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]
-0.4920.0150.745-0.24
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it4.541
p_scbond_it3.068
p_planar_tor2.907
p_mcangle_it2.773
p_angle_d2.045
p_mcbond_it1.572
p_chiral_restr0.124
p_bond_d0.012
p_plane_restr0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8216
Nucleic Acid Atoms
Solvent Atoms568
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
TRUNCATEdata scaling