4ICH

Crystal structure of a putative TetR family transcriptional regulator from Saccharomonospora viridis DSM 43017


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2 M Sodium Bromide, 0.1 M Bis Tris propane, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0540.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.845α = 90
b = 76.929β = 90
c = 109.258γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBeryllium lenses2012-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.953099.80.06542.97.45091650916-339.3
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)
11.951.981000.442.63.82515

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.9528.642572425724135999.610.201010.198580.24705RANDOM38.588
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]
0.051.27-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.506
r_dihedral_angle_4_deg17.318
r_dihedral_angle_3_deg15.36
r_dihedral_angle_1_deg2.775
r_angle_refined_deg2.007
r_angle_other_deg1.932
r_chiral_restr0.118
r_bond_refined_d0.02
r_gen_planes_refined0.014
r_gen_planes_other0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.506
r_dihedral_angle_4_deg17.318
r_dihedral_angle_3_deg15.36
r_dihedral_angle_1_deg2.775
r_angle_refined_deg2.007
r_angle_other_deg1.932
r_chiral_restr0.118
r_bond_refined_d0.02
r_gen_planes_refined0.014
r_gen_planes_other0.013
r_bond_other_d0.008
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3182
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms33

Software

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