4E1T

X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E1SPDB ENTRY 4E1S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE MONOOLEIN42940.05 M sodium citrate, pH 3.8-4.4, 0.2 M lithium sulfate, 23-35% PEG400, LIPIDIC CUBIC PHASE MONOOLEIN, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.957.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.404α = 90
b = 124.885β = 90
c = 65.073γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDK-B pair of biomorph mirrors2011-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.034375APS23-ID-B

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
12.26367.00792.70.1338.25.115222141112.32.3
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)
12.2632.3876.20.5992.91133

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 4E1S2.26329.787152221401670990.550.19150.19150.1880.2596RANDOM50.288
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]
1.461.15-2.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.565
r_dihedral_angle_4_deg21.553
r_dihedral_angle_3_deg17.787
r_dihedral_angle_1_deg6.926
r_scangle_it3.913
r_scbond_it2.566
r_angle_refined_deg1.954
r_mcangle_it1.444
r_mcbond_it0.782
r_chiral_restr0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.565
r_dihedral_angle_4_deg21.553
r_dihedral_angle_3_deg17.787
r_dihedral_angle_1_deg6.926
r_scangle_it3.913
r_scbond_it2.566
r_angle_refined_deg1.954
r_mcangle_it1.444
r_mcbond_it0.782
r_chiral_restr0.13
r_bond_refined_d0.017
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1960
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms283

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection