6EHD

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1 M NaCl, 0.1 M MES, 33% v/v PEG 400, 4% v/v ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
3.4664

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.88α = 90
b = 75.84β = 92.06
c = 49.67γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M-F2016-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9282DiamondI04

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
11.6649.64990.0220.914.53.462456
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)
11.6697.90.610.51.12.5

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 REPLACEMENTTHROUGHOUT6EHB1.6649.6459541291599.130.187720.186480.21397RANDOM39.331
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]
3.12-0.63-1.49-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.626
r_dihedral_angle_4_deg17.782
r_dihedral_angle_3_deg14.299
r_long_range_B_refined9.543
r_long_range_B_other9.485
r_dihedral_angle_1_deg7.536
r_scangle_other7.146
r_mcangle_it5.556
r_mcangle_other5.556
r_scbond_it4.921
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.626
r_dihedral_angle_4_deg17.782
r_dihedral_angle_3_deg14.299
r_long_range_B_refined9.543
r_long_range_B_other9.485
r_dihedral_angle_1_deg7.536
r_scangle_other7.146
r_mcangle_it5.556
r_mcangle_other5.556
r_scbond_it4.921
r_scbond_other4.91
r_mcbond_it4.172
r_mcbond_other4.165
r_angle_refined_deg2.185
r_angle_other_deg1.063
r_chiral_restr0.147
r_bond_refined_d0.024
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2489
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms147

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing