2GSK

Structure of the BtuB:TonB Complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NQHPDB ENTRY 1NQH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.128830% (v/v) PEG 300, 0.1M sodium acetate , pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 288K, pH 5.10
Crystal Properties
Matthews coefficientSolvent content
2.550.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.34α = 90
b = 82.439β = 90
c = 122.632γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2005-10-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

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
12.0984098.20.07811.94.644005
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)
12.12.1890.50.4362.9

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 1NQH2.1404395343953119198.10.1970.1970.1960.251RANDOM28.33
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]
0.94-0.27-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.594
r_dihedral_angle_4_deg20.607
r_dihedral_angle_3_deg15.813
r_dihedral_angle_1_deg7.454
r_scangle_it4.494
r_scbond_it3.249
r_angle_refined_deg2.223
r_mcangle_it1.97
r_mcbond_it1.281
r_angle_other_deg1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.594
r_dihedral_angle_4_deg20.607
r_dihedral_angle_3_deg15.813
r_dihedral_angle_1_deg7.454
r_scangle_it4.494
r_scbond_it3.249
r_angle_refined_deg2.223
r_mcangle_it1.97
r_mcbond_it1.281
r_angle_other_deg1.04
r_mcbond_other0.377
r_symmetry_vdw_other0.272
r_symmetry_vdw_refined0.257
r_nbd_other0.215
r_nbd_refined0.211
r_xyhbond_nbd_refined0.203
r_nbtor_refined0.19
r_xyhbond_nbd_other0.14
r_metal_ion_refined0.138
r_chiral_restr0.127
r_nbtor_other0.098
r_symmetry_hbond_refined0.073
r_bond_refined_d0.025
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_metal_ion_other
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 Atoms5194
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms190

Software

Software
Software NamePurpose
MAR345data collection
SERGUIdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement