2BON

Structure of an Escherichia coli lipid kinase (YegS)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.515% PEG 3350 0.1 M BIS-TRIS PH 5.5 0.2 M MGCL2 PLUS 15%PEG400 AS CRYOPROTECTANT.
Crystal Properties
Matthews coefficientSolvent content
2.447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.326α = 90
b = 166.164β = 97.03
c = 48.474γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM-4TOROIDAL MIRROR2004-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.939, 0.939ESRFID14-4

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
11.94897.70.06122.63825332
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)
11.92960.32.12.3

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 DIFFRACTIONSADTHROUGHOUTNONE1.983.0436269198473.40.2220.220.267RANDOM66.89
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]
90.32-4.71-4.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.573
r_dihedral_angle_4_deg20.209
r_dihedral_angle_3_deg19.845
r_dihedral_angle_1_deg7.182
r_scangle_it3.208
r_scbond_it2.135
r_angle_refined_deg1.608
r_mcangle_it1.358
r_mcbond_it0.883
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.573
r_dihedral_angle_4_deg20.209
r_dihedral_angle_3_deg19.845
r_dihedral_angle_1_deg7.182
r_scangle_it3.208
r_scbond_it2.135
r_angle_refined_deg1.608
r_mcangle_it1.358
r_mcbond_it0.883
r_nbtor_refined0.307
r_nbd_refined0.219
r_symmetry_vdw_refined0.21
r_symmetry_hbond_refined0.206
r_xyhbond_nbd_refined0.145
r_chiral_restr0.113
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4142
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing