3FGN

Crystal structure of dethiobiotin synthetase in Mycobacterium tuberculosis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52911M sodium citrate, 0.1M imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1743.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.383α = 90
b = 104.684β = 90
c = 151.392γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOTHER1.541

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
11.8531.7990.05917.24.473740
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)
11.851.9593.70.51.42.7

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 DIFFRACTIONSADTHROUGHOUT1.8531.770111370597.120.216320.214360.25332RANDOM35.247
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]
1.480.8-2.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.979
r_dihedral_angle_4_deg21.881
r_dihedral_angle_3_deg19.127
r_scangle_it6.161
r_dihedral_angle_1_deg5.822
r_scbond_it4.588
r_mcangle_it3.196
r_mcbond_it2.295
r_angle_refined_deg1.26
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.979
r_dihedral_angle_4_deg21.881
r_dihedral_angle_3_deg19.127
r_scangle_it6.161
r_dihedral_angle_1_deg5.822
r_scbond_it4.588
r_mcangle_it3.196
r_mcbond_it2.295
r_angle_refined_deg1.26
r_nbtor_refined0.308
r_symmetry_hbond_refined0.246
r_symmetry_vdw_refined0.228
r_nbd_refined0.208
r_xyhbond_nbd_refined0.18
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6318
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling