4D64

Structure of porin Omp-Pst1 from P. stuartii; the crystallographic symmetry generates a dimer of trimers.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OPFMODELLER-MODEL OF OMP-PST1 BASED ON PDB ENTRY 1OPF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.514% PEG6000 MME, 0.1 M BUFFER MES PH6.5, 0.1 M MGCL2
Crystal Properties
Matthews coefficientSolvent content
3.9468.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.52α = 90
b = 142.02β = 131
c = 113.32γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2012-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
13.25090.50.1210.982.6827279253.11
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)
13.23.2893.20.5922.66

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTMODELLER-MODEL OF OMP-PST1 BASED ON PDB ENTRY 1OPF3.236.2541.9927270136491.160.21020.20750.261143.916
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]
9.41219.1876-8.4621-0.9499
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.243
f_angle_d1.007
f_chiral_restr0.074
f_bond_d0.006
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8271
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms1

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing