8C5P

E. coli NfsB mutant N71S T41L with acetate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629110-18% PEG 4000, 50-200 mM sodium acetate buffer pH 4.6, 15% ethylene glycol.
Crystal Properties
Matthews coefficientSolvent content
2.2545.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.223α = 90
b = 57.223β = 90
c = 262.944γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2017-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9334ESRFID14-1

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
11.6947.92990.0536.91349521
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)
11.691.80.3483.54

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 REPLACEMENTTHROUGHOUT1.6943.1647036249998.990.151890.150.18793RANDOM16.507
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]
-0.54-0.541.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.566
r_long_range_B_refined6.434
r_long_range_B_other6.21
r_dihedral_angle_2_deg6.004
r_dihedral_angle_1_deg5.818
r_scangle_other5.075
r_scbond_it3.439
r_scbond_other3.439
r_mcangle_it2.805
r_mcangle_other2.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.566
r_long_range_B_refined6.434
r_long_range_B_other6.21
r_dihedral_angle_2_deg6.004
r_dihedral_angle_1_deg5.818
r_scangle_other5.075
r_scbond_it3.439
r_scbond_other3.439
r_mcangle_it2.805
r_mcangle_other2.805
r_mcbond_it2.161
r_mcbond_other2.139
r_angle_refined_deg1.818
r_angle_other_deg0.621
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.014
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms3352
Nucleic Acid Atoms
Solvent Atoms527
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing