5X7L

Structure of TsrD from Streptomyces laurentii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, and 30% v/v 2-Propanol
Crystal Properties
Matthews coefficientSolvent content
2.7555.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.232α = 90
b = 54.232β = 90
c = 199.952γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORDECTRIS PILATUS 6M2016-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNFPSS BEAMLINE BL19U10.98NFPSSBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.225099.638.318.9102592

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 DIFFRACTIONSADTHROUGHOUT1.2238.4295308501397.880.15140.150620.16631RANDOM17.411
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]
-0.08-0.08-0.080.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.208
r_sphericity_free20.396
r_dihedral_angle_4_deg12.842
r_dihedral_angle_3_deg10.012
r_sphericity_bonded7.536
r_dihedral_angle_1_deg4.776
r_long_range_B_refined2.404
r_long_range_B_other2.404
r_rigid_bond_restr1.905
r_angle_other_deg1.439
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.208
r_sphericity_free20.396
r_dihedral_angle_4_deg12.842
r_dihedral_angle_3_deg10.012
r_sphericity_bonded7.536
r_dihedral_angle_1_deg4.776
r_long_range_B_refined2.404
r_long_range_B_other2.404
r_rigid_bond_restr1.905
r_angle_other_deg1.439
r_scangle_other1.368
r_mcangle_other1.221
r_mcangle_it1.217
r_scbond_it1.033
r_scbond_other1.033
r_angle_refined_deg0.978
r_mcbond_other0.843
r_mcbond_it0.835
r_chiral_restr0.052
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2091
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data processing