4K3F

Crystal structure of a putative TonB-dependent receptor (PA5505) from Pseudomonas aeruginosa PAO1 at 1.60 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72933.20M ammonium sulfate, 0.7% n-Butanol, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.577α = 90
b = 40.509β = 90
c = 60.813γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MRhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator2013-04-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.8265,0.9794,0.9792SSRLBL12-2

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
11.629.13592.40.0569.1632359-319.747
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)
11.61.6692.10.4671.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.629.13532319164197.070.15230.15060.1847RANDOM22.2558
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]
0.95-0.68-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.163
r_dihedral_angle_4_deg15.994
r_dihedral_angle_3_deg13.063
r_dihedral_angle_1_deg5.903
r_mcangle_it2.415
r_mcbond_other1.827
r_mcbond_it1.826
r_angle_refined_deg1.536
r_angle_other_deg0.812
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.163
r_dihedral_angle_4_deg15.994
r_dihedral_angle_3_deg13.063
r_dihedral_angle_1_deg5.903
r_mcangle_it2.415
r_mcbond_other1.827
r_mcbond_it1.826
r_angle_refined_deg1.536
r_angle_other_deg0.812
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1832
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms50

Software

Software
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
SHELXDphasing