3CJN

Crystal structure of transcriptional regulator, MarR family, from Silicibacter pomeroyi


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72810.1 Succinic acid pH 7.0, 12 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.2645.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.976α = 90
b = 87.976β = 90
c = 43.197γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97935APS19-ID

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
11.95501000.09477.2211294412941-328
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)
11.952.021000.47214.521.81263

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.9543.98128191281962499.20.181190.181190.179120.22257RANDOM32.927
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]
-0.75-0.751.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.835
r_dihedral_angle_4_deg17.392
r_dihedral_angle_3_deg12.965
r_dihedral_angle_1_deg5.126
r_scangle_it2.881
r_scbond_it2.006
r_mcangle_it1.329
r_angle_refined_deg1.282
r_mcbond_it0.857
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.835
r_dihedral_angle_4_deg17.392
r_dihedral_angle_3_deg12.965
r_dihedral_angle_1_deg5.126
r_scangle_it2.881
r_scbond_it2.006
r_mcangle_it1.329
r_angle_refined_deg1.282
r_mcbond_it0.857
r_nbtor_refined0.303
r_symmetry_vdw_refined0.266
r_nbd_refined0.21
r_symmetry_hbond_refined0.176
r_xyhbond_nbd_refined0.132
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1133
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing