2REK

Crystal structure of tetR-family transcriptional regulator


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62970.1M Na(OAC) pH 4.6, 2.0M Na formate, 4% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.0840.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.484α = 90
b = 70.459β = 90
c = 72.102γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVVariMax Cr2006-07-07MSINGLE WAVELENGTH
21x-ray100IMAGE PLATERIGAKU RAXIS IVVariMax HR2006-08-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2002.29
2ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1,21.8650.3899.90.0520.052127.1300583005834.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.861.891000.5170.5173.116.91467

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 DIFFRACTIONSADTHROUGHOUT1.8650.38293812938162699.90.203960.203960.20310.24506RANDOM36.254
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]
-1.261.55-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.932
r_dihedral_angle_3_deg13.738
r_dihedral_angle_4_deg11.053
r_dihedral_angle_1_deg4.348
r_scangle_it3.901
r_scbond_it2.425
r_mcangle_it1.478
r_angle_refined_deg1.185
r_mcbond_it0.875
r_nbtor_refined0.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.932
r_dihedral_angle_3_deg13.738
r_dihedral_angle_4_deg11.053
r_dihedral_angle_1_deg4.348
r_scangle_it3.901
r_scbond_it2.425
r_mcangle_it1.478
r_angle_refined_deg1.185
r_mcbond_it0.875
r_nbtor_refined0.291
r_nbd_refined0.198
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.141
r_chiral_restr0.083
r_bond_refined_d0.011
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 Atoms2470
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building