3EH0

Crystal Structure of LpxD from Escherichia coli


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.42900.1 M MES, 2.0 M (NH4)2SO4, 1% doixane, 1 mM DTT, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthew coefficientSolvent content
2.8757.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.95α = 90
b = 94.17β = 126.5
c = 103.66γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.65096.70.1140.16810.63.3381243686311
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)
2.62.7497.20.443.13.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUThomology model based on pdb code 2IUA2.620223705335182187198.510.216890.213650.27911RANDOM43.271
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]
0.68-1.18-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.058
r_dihedral_angle_4_deg18.456
r_dihedral_angle_3_deg13.652
r_scangle_it6.471
r_dihedral_angle_1_deg6.405
r_mcangle_it4.534
r_scbond_it4.281
r_mcbond_it3.352
r_angle_refined_deg1.49
r_symmetry_vdw_refined0.452
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.058
r_dihedral_angle_4_deg18.456
r_dihedral_angle_3_deg13.652
r_scangle_it6.471
r_dihedral_angle_1_deg6.405
r_mcangle_it4.534
r_scbond_it4.281
r_mcbond_it3.352
r_angle_refined_deg1.49
r_symmetry_vdw_refined0.452
r_nbtor_refined0.329
r_symmetry_hbond_refined0.296
r_nbd_refined0.248
r_xyhbond_nbd_refined0.156
r_chiral_restr0.093
r_bond_refined_d0.015
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7553
Nucleic Acid Atoms
Solvent Atoms365
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling