3FMS

Crystal structure of TM0439, a GntR transcriptional regulator


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529335% 2-methyl-2,4-pentanediol, 0.1 M Sodium acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6152.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.188α = 90
b = 71.718β = 104.59
c = 43.323γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173CCDADSC QUANTUM 3152007-08-10MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.10.97960, 0.95370, 0.97980ALS8.2.1

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
12.24098.40.05146.3712695
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)
12.22.2888.30.2285.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.236.1631.391258662097.610.1610.1570.22838.632
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]
-2.7293.6370.8651.864
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.195
f_angle_d1.31
f_chiral_restr0.108
f_bond_d0.017
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1713
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms9

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing