6RNZ

Crystal structure of the N-terminal HTH DNA-binding domain of the essential repressor DdrO from radiation-resistant Deinococcus bacteria (Deinococcus deserti)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M Bis-Tris propane pH 7, 2.5 M Ammonium Sulfate
Crystal Properties
Matthew coefficientSolvent content
2.4249.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.257α = 90
b = 43.227β = 106.66
c = 45.87γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2016-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.9660ESRFMASSIF-1

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
11.354498.30.04810.92.831092
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.4

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 REPLACEMENTTHROUGHOUT6RNX1.3543.9429520155898.20.131140.12870.17701RANDOM16.675
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]
0.26-0.31-0.230.13
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.979
r_dihedral_angle_2_deg31.905
r_dihedral_angle_4_deg23.005
r_dihedral_angle_3_deg13.594
r_sphericity_bonded12.856
r_long_range_B_refined6.156
r_long_range_B_other6.154
r_rigid_bond_restr5.473
r_scangle_other4.55
r_dihedral_angle_1_deg4.242
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free38.979
r_dihedral_angle_2_deg31.905
r_dihedral_angle_4_deg23.005
r_dihedral_angle_3_deg13.594
r_sphericity_bonded12.856
r_long_range_B_refined6.156
r_long_range_B_other6.154
r_rigid_bond_restr5.473
r_scangle_other4.55
r_dihedral_angle_1_deg4.242
r_scbond_other3.903
r_scbond_it3.897
r_angle_refined_deg2.375
r_mcangle_it1.909
r_mcangle_other1.909
r_mcbond_it1.694
r_mcbond_other1.69
r_angle_other_deg1.477
r_chiral_restr0.159
r_bond_refined_d0.029
r_gen_planes_refined0.013
r_gen_planes_other0.005
r_bond_other_d0.002
r_xyhbond_nbd_refined
r_symmetry_metal_ion_other
r_symmetry_vdw_other
r_metal_ion_other
r_metal_ion_refined
r_xyhbond_nbd_other
r_symmetry_hbond_refined
r_nbtor_other
r_scangle_it
r_nbtor_refined
r_nbd_other
r_nbd_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1054
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
AutoPROCdata scaling
MOLREPphasing