5UDG

Mutant E97Q crystal structure of Bacillus subtilis QueF with a disulfide Cys 55-99


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Protein sample 4 mg/mL, in 50 mM Tris pH 7.5, 50 mM KCl, 1 mM MgCl2 and 1 mM (mercaptoethanol-BME) was mixed with reservoir solution (1:1 ratio) containing 19% PEG 550 monomethyl ether, 43 mM imidazole-Cl (pH 6.8), 53 mM imidazole (pH 8.2), 30 mM CaCl2, and 4% DMSO
Crystal Properties
Matthews coefficientSolvent content
2.5151

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.308α = 90
b = 87.308β = 90
c = 196.734γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2012-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-21.1SSRLBL12-2

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
12.545.61980.1211453029850
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5489.40.830.753

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4F8B2.545.6128711151697.860.199060.194280.29339RANDOM47.938
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]
1.810.911.81-2.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.09
r_dihedral_angle_3_deg18.641
r_dihedral_angle_4_deg17.148
r_dihedral_angle_1_deg7.34
r_angle_refined_deg1.579
r_chiral_restr0.106
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.09
r_dihedral_angle_3_deg18.641
r_dihedral_angle_4_deg17.148
r_dihedral_angle_1_deg7.34
r_angle_refined_deg1.579
r_chiral_restr0.106
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6065
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing