2OGG

Structure of B. subtilis trehalose repressor (TreR) effector binding domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298Reservoir: 0.1M MES pH 6.0, 1.26M Ammonium sulfate, 0.56mM CYMAL-5. Protein: 21.2mg/ml. Drops: 1+1 microliter, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.9869.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.719α = 90
b = 69.719β = 90
c = 236.535γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97900APS19-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
12.55095.60.065061012658.7
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)
12.52.5470.50.2783.23.9

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 DIFFRACTIONSADTHROUGHOUT2.537.88101261012699095.640.195760.195760.190240.24659RANDOM43.687
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]
-0.71-0.711.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.337
r_dihedral_angle_3_deg17.082
r_dihedral_angle_4_deg14.926
r_scangle_it9.32
r_scbond_it7.027
r_dihedral_angle_1_deg6.938
r_mcangle_it3.73
r_mcbond_it2.28
r_angle_refined_deg1.412
r_chiral_restr0.358
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.337
r_dihedral_angle_3_deg17.082
r_dihedral_angle_4_deg14.926
r_scangle_it9.32
r_scbond_it7.027
r_dihedral_angle_1_deg6.938
r_mcangle_it3.73
r_mcbond_it2.28
r_angle_refined_deg1.412
r_chiral_restr0.358
r_nbtor_refined0.337
r_nbd_refined0.281
r_symmetry_vdw_refined0.264
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.159
r_gen_planes_refined0.025
r_bond_refined_d0.013
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 Atoms1213
Nucleic Acid Atoms
Solvent Atoms36
Heterogen Atoms29

Software

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