8OG3

E. coli NfsB triple mutant T41L/N71S/F124T bound to citrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ICR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629113% PEG 4,000; 100 mM Na Acetate, 15% Ethylene glycol, 100 mM Citrate
Crystal Properties
Matthews coefficientSolvent content
2.2845.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.263α = 90
b = 57.263β = 90
c = 263.827γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2010-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.933ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.0947.9999.80.08321.177.1627043
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.0942.14898.450.3695.54

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.0947.9925696134799.880.167170.164510.21796RANDOM21.551
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]
-0.89-0.891.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.155
r_dihedral_angle_2_deg7.449
r_long_range_B_refined7.005
r_long_range_B_other7.004
r_dihedral_angle_1_deg6.163
r_scangle_other5.452
r_scbond_it3.62
r_scbond_other3.578
r_mcangle_it3.446
r_mcangle_other3.445
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.155
r_dihedral_angle_2_deg7.449
r_long_range_B_refined7.005
r_long_range_B_other7.004
r_dihedral_angle_1_deg6.163
r_scangle_other5.452
r_scbond_it3.62
r_scbond_other3.578
r_mcangle_it3.446
r_mcangle_other3.445
r_mcbond_it2.431
r_mcbond_other2.431
r_angle_refined_deg1.589
r_angle_other_deg0.541
r_chiral_restr0.075
r_gen_planes_refined0.011
r_bond_refined_d0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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 Atoms3346
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing