3BWG

The crystal structure of possible transcriptional regulator YydK from Bacillus subtilis subsp. subtilis str. 168


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52890.1M Ammonium acetate, 0.1M Bis-Tris, 17% PEG 10000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3347.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.994α = 90
b = 58.284β = 110.08
c = 138.823γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2007-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-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
12.0943.9889.50.0723.83.34058040580
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)
12.092.1843.30.441.652.21941

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 DIFFRACTIONSADTHROUGHOUT2.0943.983942239422206491.490.188510.188510.186440.22846RANDOM43.851
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]
0.550.350.25-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.763
r_dihedral_angle_4_deg22.046
r_dihedral_angle_3_deg18.895
r_dihedral_angle_1_deg7.43
r_mcangle_it2.149
r_scangle_it1.999
r_angle_refined_deg1.677
r_scbond_it1.454
r_mcbond_it1.383
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.763
r_dihedral_angle_4_deg22.046
r_dihedral_angle_3_deg18.895
r_dihedral_angle_1_deg7.43
r_mcangle_it2.149
r_scangle_it1.999
r_angle_refined_deg1.677
r_scbond_it1.454
r_mcbond_it1.383
r_nbtor_refined0.306
r_nbd_refined0.217
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.141
r_chiral_restr0.12
r_bond_refined_d0.016
r_gen_planes_refined0.006
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 Atoms5496
Nucleic Acid Atoms
Solvent Atoms288
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing