3NYS

X-ray structure of the K185A mutant of WbpE (WlbE) from pseudomonas aeruginosa in complex with PLP at 1.45 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FRKPDB ENTRY 3FRK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629825% pentaerythritrol propoxylate, 100 mM MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3146.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.783α = 90
b = 93.57β = 115.58
c = 77.067γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135mondel2010-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.54178

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
11.453097.20.0610.06112.956236262362
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.4892.90.320.322.72.22316

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3FRK1.45306233059196316397.210.171610.171610.170020.20085RANDOM14.169
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]
0.460.350.05-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.588
r_dihedral_angle_4_deg19.877
r_dihedral_angle_3_deg12.307
r_dihedral_angle_1_deg6.32
r_scangle_it5.312
r_scbond_it3.611
r_mcangle_it2.405
r_angle_refined_deg2.003
r_mcbond_it1.598
r_chiral_restr0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.588
r_dihedral_angle_4_deg19.877
r_dihedral_angle_3_deg12.307
r_dihedral_angle_1_deg6.32
r_scangle_it5.312
r_scbond_it3.611
r_mcangle_it2.405
r_angle_refined_deg2.003
r_mcbond_it1.598
r_chiral_restr0.144
r_bond_refined_d0.014
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2729
Nucleic Acid Atoms
Solvent Atoms485
Heterogen Atoms17

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
SADABSdata scaling