4TV7

Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293PEG 1000, PEG 400, ethyleneglycol, calcium acetate, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.5852.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.831α = 90
b = 101.556β = 90
c = 212.987γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

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
12.055097.30.05916.26.1130131
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)
12.052.0995.60.585.46302

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.0547.67123479656497.30.233810.231110.28442RANDOM52.039
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]
0.59-0.4-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.525
r_dihedral_angle_4_deg20.283
r_dihedral_angle_3_deg17.522
r_long_range_B_refined8.515
r_dihedral_angle_1_deg5.941
r_mcangle_it4.902
r_scbond_it4.044
r_mcbond_it3.425
r_angle_refined_deg1.449
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.525
r_dihedral_angle_4_deg20.283
r_dihedral_angle_3_deg17.522
r_long_range_B_refined8.515
r_dihedral_angle_1_deg5.941
r_mcangle_it4.902
r_scbond_it4.044
r_mcbond_it3.425
r_angle_refined_deg1.449
r_chiral_restr0.098
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13936
Nucleic Acid Atoms
Solvent Atoms563
Heterogen Atoms

Software

Software
Software NamePurpose
HKL-2000data reduction
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
RESOLVEmodel building
REFMACrefinement
SOLVEmodel building
REFMAC5refinement
HKLdata scaling