5HS7

Reduced form of the transcriptional regulator YodB from B. subtilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HQM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.2M sodium bromide and 20%(w/v) PEG 3,350
Crystal Properties
Matthews coefficientSolvent content
2.0439.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.78α = 90
b = 50.798β = 95.49
c = 50.354γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702015-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 7A (6B, 6C1)1.0000PAL/PLS7A (6B, 6C1)

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
11.750.12990.05644.56.222351
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)
11.71.730.451

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4HQM1.750.1221301103598.720.198180.197020.22077RANDOM30.782
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]
-0.61-11.07-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.229
r_dihedral_angle_3_deg13.365
r_dihedral_angle_4_deg12.673
r_long_range_B_refined7.4
r_long_range_B_other7.156
r_dihedral_angle_1_deg5.076
r_scangle_other4.61
r_mcangle_it3.438
r_mcangle_other3.437
r_scbond_it2.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.229
r_dihedral_angle_3_deg13.365
r_dihedral_angle_4_deg12.673
r_long_range_B_refined7.4
r_long_range_B_other7.156
r_dihedral_angle_1_deg5.076
r_scangle_other4.61
r_mcangle_it3.438
r_mcangle_other3.437
r_scbond_it2.935
r_scbond_other2.933
r_mcbond_it2.239
r_mcbond_other2.235
r_angle_refined_deg1.539
r_angle_other_deg0.945
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1610
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing