6EHF

OmpT (in-vitro folded), an outer membrane protein Vibrio cholerae (trimer form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6EHD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.22980.05 M calcium chloride dihydrate, 0.05 M barium chloride, 0.1 M tris, 32% PEG 400
Crystal Properties
Matthews coefficientSolvent content
4.4572.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 200.91α = 90
b = 200.91β = 90
c = 200.91γ = 90
Symmetry
Space GroupI 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M-F2016-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9762DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
12.7271.03990.025122.142.218714
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72980.6790.61.243.7

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6EHD2.7271.031774795698.980.240150.237980.28059RANDOM96.065
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.924
r_dihedral_angle_4_deg26.628
r_dihedral_angle_3_deg17.646
r_long_range_B_refined13.903
r_long_range_B_other13.901
r_scangle_other11.67
r_mcangle_it10.552
r_mcangle_other10.549
r_dihedral_angle_1_deg9.045
r_scbond_it8.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.924
r_dihedral_angle_4_deg26.628
r_dihedral_angle_3_deg17.646
r_long_range_B_refined13.903
r_long_range_B_other13.901
r_scangle_other11.67
r_mcangle_it10.552
r_mcangle_other10.549
r_dihedral_angle_1_deg9.045
r_scbond_it8.333
r_scbond_other8.333
r_mcbond_it7.629
r_mcbond_other7.629
r_angle_refined_deg1.91
r_angle_other_deg1.036
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2451
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing