8QES

E coli NfsB with the unnatural amino acid, p-aminoPhe at position 124


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.6291100 mM Sodium acetate, pH 4.6, 15 mM nicotinic acid, 15% Ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.448.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.45α = 90
b = 57.96β = 103.73
c = 116.49γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

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
12.4853.8199.60.09411.53.443294914.16
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)
12.482.54899.30.26

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 REPLACEMENTTHROUGHOUT2.4853.8130944199199.630.164420.161480.20989RANDOM23.997
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]
1.73-0.6-0.22-1.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.343
r_long_range_B_refined7.905
r_long_range_B_other7.904
r_scangle_other6.797
r_dihedral_angle_1_deg6.211
r_dihedral_angle_2_deg5.916
r_mcangle_it4.999
r_mcangle_other4.998
r_scbond_it4.625
r_scbond_other4.625
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.343
r_long_range_B_refined7.905
r_long_range_B_other7.904
r_scangle_other6.797
r_dihedral_angle_1_deg6.211
r_dihedral_angle_2_deg5.916
r_mcangle_it4.999
r_mcangle_other4.998
r_scbond_it4.625
r_scbond_other4.625
r_mcbond_it3.464
r_mcbond_other3.461
r_angle_refined_deg1.886
r_angle_other_deg0.631
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.014
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 Atoms6712
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms160

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
pointlessdata scaling
PHASERphasing