8PQM

The DNA-binding domain of L-lactate utilization repressor (LutR-DBD) from Bacillus subtilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelITasser 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291Morpheus screen solution: 0.1 M sodium HEPES/MOPS (acid) buffer system (pH 7.5), 37.5% (v/v) 2 methyl 2,4 pentanediol, 37.5% (v/v) PEG 1000, 37.5% (v/v) PEG 3350, 0.03 M NaF, 0.03 M NaBr, 0.03 M NaI Volume ratio (protein:solution) = 1ul : 2ul Plate: EasyXtal 15 well plate (NeXtal Biotechnologies, Holland)
Crystal Properties
Matthews coefficientSolvent content
1.7930.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 28.31α = 90
b = 38.37β = 90
c = 66.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9797BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.46501000.0670.0730.999000000000000112.266.7624387
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.553.11899999999999983.3880.319

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4633.381252766099.980.204020.202210.20860.237350.239RANDOM40.221
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]
0.77-0.950.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.925
r_dihedral_angle_2_deg13.993
r_long_range_B_refined13.299
r_long_range_B_other13.038
r_scangle_other7.679
r_mcangle_it7.112
r_mcangle_other7.111
r_dihedral_angle_1_deg6.272
r_scbond_other5.15
r_scbond_it5.147
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms593
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing