4OQQ

Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52910.1 M Bicine, 20% (w/v) PEG 6000; 12.5 mg/mL protein in 20 mM trisodium citrate pH 7.0, 150 mM NaCl, 0.02% (v/v) 2-mercaptoethanol; protein:reservoir 1:2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.9458.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.081α = 90
b = 63.081β = 90
c = 150.129γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDouble crystal monochromator with 2 sets of Rh-soated silicon and glass mirrors2012-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

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
11.85093.10.0483.86217757887
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8653.30.1792.92.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4OQP1.827.316217754842292192.870.194550.192760.22756RANDOM52.488
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.194
r_dihedral_angle_4_deg16.52
r_dihedral_angle_3_deg12.636
r_long_range_B_refined6.277
r_long_range_B_other6.276
r_dihedral_angle_1_deg5.788
r_scangle_other2.851
r_mcangle_it2.234
r_mcangle_other2.072
r_scbond_it2.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.194
r_dihedral_angle_4_deg16.52
r_dihedral_angle_3_deg12.636
r_long_range_B_refined6.277
r_long_range_B_other6.276
r_dihedral_angle_1_deg5.788
r_scangle_other2.851
r_mcangle_it2.234
r_mcangle_other2.072
r_scbond_it2.014
r_scbond_other1.863
r_mcbond_it1.513
r_mcbond_other1.513
r_angle_refined_deg1.439
r_angle_other_deg0.79
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3970
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms22

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling