1ZWL

Structure of WrbA from Pseudomonas aeruginosa in complex with FMN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YDG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629316% PEG 3350, .12M MgCl, .1M Bis pH 6.0, .003M FMN, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8155.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.54α = 90
b = 73.54β = 90
c = 78.166γ = 90
Symmetry
Space GroupP 42 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9791NSLSX29A

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
12.82099.20.1114.86.256165616-3
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)
12.82.993.30.2770.05123.934.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT1YDG2.820-35602560225398.780.198580.198580.196930.23594RANDOM57.496
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]
2.082.08-4.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.531
r_dihedral_angle_4_deg22.168
r_dihedral_angle_3_deg16.86
r_dihedral_angle_1_deg5.701
r_scangle_it2.225
r_angle_refined_deg1.334
r_scbond_it1.279
r_mcangle_it1.238
r_mcbond_it0.687
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.531
r_dihedral_angle_4_deg22.168
r_dihedral_angle_3_deg16.86
r_dihedral_angle_1_deg5.701
r_scangle_it2.225
r_angle_refined_deg1.334
r_scbond_it1.279
r_mcangle_it1.238
r_mcbond_it0.687
r_nbtor_refined0.308
r_symmetry_vdw_refined0.241
r_nbd_refined0.219
r_xyhbond_nbd_refined0.189
r_symmetry_hbond_refined0.116
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1277
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing