8CJ0

E. coli NfsB-T41Q/N71S/F124T/M127V mutant bound to nicotinate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ICRwild type NfsB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629112% PEG 4000, 100 mM Na Acetate, 20 mM Nicotinic acid, 15% Ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.2946.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.31α = 90
b = 57.31β = 90
c = 265.67γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2009-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

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
11.9935.0698.90.07525.3931129
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)
11.9942.04695.40.558.93

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 REPLACEMENTTHROUGHOUT1.9935.0629553157598.880.162830.160950.19869RANDOM38.944
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]
-0.04-0.040.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.675
r_long_range_B_other11.808
r_long_range_B_refined11.792
r_scangle_other10.176
r_scbond_other7.44
r_scbond_it7.438
r_dihedral_angle_1_deg6.123
r_mcangle_other5.442
r_mcangle_it5.425
r_mcbond_it4.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.675
r_long_range_B_other11.808
r_long_range_B_refined11.792
r_scangle_other10.176
r_scbond_other7.44
r_scbond_it7.438
r_dihedral_angle_1_deg6.123
r_mcangle_other5.442
r_mcangle_it5.425
r_mcbond_it4.057
r_mcbond_other4.056
r_angle_refined_deg1.275
r_angle_other_deg0.49
r_chiral_restr0.069
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_2_deg
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 Atoms3344
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms84

Software

Software
Software NamePurpose
PDB-REDOrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing