3MC8

POTRA1-3 of the periplasmic domain of Omp85 from Anabaena


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52920.1 M Tris buffer, 0.8 M Na/K Tartrate, 0.5% PEG-MME 5000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.3262.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.268α = 90
b = 105.268β = 90
c = 83.278γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rLIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR AND A CYLINDRICAL GRAZING INCIDENCE MIRROR2008-09-04MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 210HORIZONTALLY BENDED GE(220)2008-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29
2SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
1,22.59501000.09926.420.315133-477.3
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)
2.592.651000.4726.918.7

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 DIFFRACTIONSADTHROUGHOUTSELENOMETHIONINE SAD PHASED MUTANT (F291M), FOLLOWED BY MR INTO NATIVE DATA.2.5950143307611000.2290.2260.281RANDOM40.82
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]
-0.82-0.821.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.429
r_dihedral_angle_3_deg20.057
r_dihedral_angle_4_deg17.116
r_dihedral_angle_1_deg6.635
r_scangle_it3.964
r_scbond_it2.189
r_angle_refined_deg1.648
r_mcangle_it1.629
r_angle_other_deg1.122
r_mcbond_it0.838
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.429
r_dihedral_angle_3_deg20.057
r_dihedral_angle_4_deg17.116
r_dihedral_angle_1_deg6.635
r_scangle_it3.964
r_scbond_it2.189
r_angle_refined_deg1.648
r_mcangle_it1.629
r_angle_other_deg1.122
r_mcbond_it0.838
r_mcbond_other0.092
r_chiral_restr0.086
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2014
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms

Software

Software
Software NamePurpose
DNAdata collection
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling