3UPG

Loop deletion mutant of Salmonella typhi osmoporin (OmpC):an Outer Membrane Protein.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JN1PDB ENTRY 2JN1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.1298.1520% Polyethylene glycol 3350, 0.2M Calcium chloride dihydrate, pH 5.1, Microbatch, temperature 298.15K
Crystal Properties
Matthews coefficientSolvent content
5.5677.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.149α = 90
b = 115.149β = 90
c = 216.736γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.03CCDMARMOSAIC 225 mm CCD2009-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97869ESRFBM14

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
13.2108.3799.10.14415.2111.51470914582
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)
13.23.3197.20.4552.255.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2JN13.250147091384673099.140.289530.287720.32456RANDOM91.449
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]
5.282.645.28-7.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.073
r_dihedral_angle_4_deg24.824
r_dihedral_angle_3_deg24.267
r_dihedral_angle_1_deg9.818
r_scangle_it2.56
r_angle_refined_deg1.701
r_scbond_it1.502
r_mcangle_it1.493
r_mcbond_it0.792
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.073
r_dihedral_angle_4_deg24.824
r_dihedral_angle_3_deg24.267
r_dihedral_angle_1_deg9.818
r_scangle_it2.56
r_angle_refined_deg1.701
r_scbond_it1.502
r_mcangle_it1.493
r_mcbond_it0.792
r_chiral_restr0.109
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2406
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms5

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling