4WY2

Crystal structure of universal stress protein E from Proteus mirabilis in complex with UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-N-acetyl-alpha-glucosamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OLQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52890.2 ul of 12 mg/ml protein in 10mM HEPES, 500mM NaCl pH 7.5 were mixed with 0.2 ul of the Quiagen Cryos Suite condition #50 (1.36 M Ammonium Sulfate, 0.085 M MES pH 6.5, 8.5% Dioxane, 15% Glycerol) and equilibrated against the mother liquor in 96 Well 2 drop Crystallization Plate (MRC)
Crystal Properties
Matthews coefficientSolvent content
359.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.877α = 90
b = 107.877β = 90
c = 74.923γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium Lenses2014-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.85099.60.080.0870.0339.56.641254-329
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8398.70.8920.9760.3890.751.96.12017

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OLQ1.85039066201998.990.17360.17210.2018RANDOM35.365
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]
-1.01-1.012.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.567
r_dihedral_angle_4_deg17.273
r_dihedral_angle_3_deg13.234
r_dihedral_angle_1_deg5.457
r_mcangle_it1.792
r_angle_refined_deg1.453
r_mcbond_other1.166
r_mcbond_it1.165
r_angle_other_deg0.776
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.567
r_dihedral_angle_4_deg17.273
r_dihedral_angle_3_deg13.234
r_dihedral_angle_1_deg5.457
r_mcangle_it1.792
r_angle_refined_deg1.453
r_mcbond_other1.166
r_mcbond_it1.165
r_angle_other_deg0.776
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2448
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms73

Software

Software
Software NamePurpose
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction