5NXN

Structure of a L5-deletion mutant of Providencia stuartii Omp-Pst1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4D64 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.527725% PEG 600, 0.2 M NaCl, 0.1 M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.766.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.321α = 90
b = 158.985β = 124.65
c = 101.326γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MToroidal mirror2016-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.93ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
13.115097.30.2020.9988.166.7829184170.279
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.113.2179.21.6810.6051.036.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4D643.125027554148198.650.247350.24620.250.267950.27RANDOM97.919
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]
3.281.50.02-2.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.119
r_dihedral_angle_3_deg20.613
r_dihedral_angle_4_deg17.314
r_long_range_B_refined10.247
r_dihedral_angle_1_deg5.041
r_mcangle_it2.837
r_angle_refined_deg1.948
r_mcbond_it1.606
r_scbond_it1.455
r_chiral_restr0.149
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8028
Nucleic Acid Atoms
Solvent Atoms520
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing