4R37

Crystal structure analysis of LpxA, a UDP-N-acetylglucosamine acyltransferase from Bacteroides fragilis 9343 with UDP-GlcNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LXAPDB entry 1LXA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529328 % PEG600, 200 mM Calcium Acetate, 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3247.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 149.403α = 90
b = 149.403β = 90
c = 149.403γ = 90
Symmetry
Space GroupP 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Rh coated flat mirror2014-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.12709SSRLBL7-1

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
11.9105.6499.90.052307.14518645186-318.6
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)
11.91.9599.50.3575.67.12959

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1LXA1.9384285242852228999.850.149280.147390.18513RANDOM21.123
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.379
r_dihedral_angle_4_deg20.874
r_dihedral_angle_3_deg12.584
r_dihedral_angle_1_deg6.724
r_long_range_B_refined6.366
r_long_range_B_other6.097
r_scangle_other4.49
r_scbond_it3.026
r_scbond_other3.025
r_mcangle_other2.285
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.379
r_dihedral_angle_4_deg20.874
r_dihedral_angle_3_deg12.584
r_dihedral_angle_1_deg6.724
r_long_range_B_refined6.366
r_long_range_B_other6.097
r_scangle_other4.49
r_scbond_it3.026
r_scbond_other3.025
r_mcangle_other2.285
r_mcangle_it2.284
r_angle_refined_deg1.798
r_mcbond_it1.742
r_mcbond_other1.726
r_angle_other_deg1.231
r_chiral_restr0.105
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3894
Nucleic Acid Atoms
Solvent Atoms517
Heterogen Atoms86

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
Aimlessdata scaling