4OQP

Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52910.08 M HEPES, 9.6% (w/v) PEG 3350, 4 mM CoCl2, 4 mM CdCl2, 4 mM MgCl2, and 4 mM NiCl2; 16.5 mg/mL protein in 20 mM trisodium citrate pH 7.0, 150 mM NaCl, 0.02% (v/v) 2-mercaptoethanol, 50 mM deoxyribose-5-phosphate; protein:reservoir 2:1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3647.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.995α = 90
b = 78.983β = 90
c = 91.338γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDOUBLE CRYSTAL MONOCHROMATOR WITH 2 SETS OF RH-SOATED SILLICON AND GLASS MIRRORS2012-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

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
11.65093.50.045.634660
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)
11.61.6662.30.2552.83.3

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 3NZE1.619.773728932880175093.40.1560.1540.191RANDOM24.6
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_deg34.758
r_dihedral_angle_4_deg17.438
r_dihedral_angle_3_deg12.846
r_long_range_B_refined6.715
r_long_range_B_other6.714
r_dihedral_angle_1_deg5.701
r_scangle_other1.782
r_angle_refined_deg1.488
r_mcangle_other1.437
r_mcangle_it1.435
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.758
r_dihedral_angle_4_deg17.438
r_dihedral_angle_3_deg12.846
r_long_range_B_refined6.715
r_long_range_B_other6.714
r_dihedral_angle_1_deg5.701
r_scangle_other1.782
r_angle_refined_deg1.488
r_mcangle_other1.437
r_mcangle_it1.435
r_scbond_it1.097
r_scbond_other1.097
r_angle_other_deg0.847
r_mcbond_it0.838
r_mcbond_other0.831
r_chiral_restr0.13
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms1988
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms18

Software

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