2IU5

Dihydroxyacetone kinase operon activator DhaS


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16THE CONCENTRATED PROTEIN (20 MG/ML) WAS MIXED WITH BUFFER CONTAINING 50 MM NA-CACODYLATE PH 6.0, 1.7 M AMMONIUM SULFATE, 0.015 M MG-ACETATE IN A 1:1 RATIO.
Crystal Properties
Matthews coefficientSolvent content
1.934.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.459α = 90
b = 46.284β = 90
c = 171.939γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM14ESRFBM14

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
11.64099.20.05164.4454923
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)
11.61.651000.180.074.01

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 DIFFRACTIONMIRASTHROUGHOUT1.64045492201399.30.1970.1950.23RANDOM23.23
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]
-0.510.9-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.076
r_dihedral_angle_4_deg24.349
r_dihedral_angle_3_deg16.38
r_dihedral_angle_1_deg5.751
r_scangle_it4.032
r_scbond_it2.601
r_mcangle_it1.901
r_angle_refined_deg1.682
r_mcbond_it1.313
r_nbtor_refined0.329
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.076
r_dihedral_angle_4_deg24.349
r_dihedral_angle_3_deg16.38
r_dihedral_angle_1_deg5.751
r_scangle_it4.032
r_scbond_it2.601
r_mcangle_it1.901
r_angle_refined_deg1.682
r_mcbond_it1.313
r_nbtor_refined0.329
r_xyhbond_nbd_refined0.241
r_nbd_refined0.239
r_symmetry_hbond_refined0.229
r_symmetry_vdw_refined0.19
r_chiral_restr0.107
r_bond_refined_d0.008
r_gen_planes_refined0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
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 Atoms3034
Nucleic Acid Atoms
Solvent Atoms294
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling