3IBZ

Crystal structure of putative tellurium resistant like protein (TerD) from Streptomyces coelicolor A3(2)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52930.1M TRIS PH8.5, 12% GLYCEROL, 1.5M NH4SO4, VAPOR DIFFUSION - SITTING DROP, TEMPERATURE 273K, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2445.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.836α = 90
b = 61.456β = 90
c = 85.713γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRROR2009-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9793APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.7849.9499.10.0710.07122.13.318188-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.811000.5540.5542.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.7849.94181231812392998.980.1640.1640.1630.2RANDOM7.48
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]
-1.8-0.282.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.288
r_dihedral_angle_4_deg23.35
r_dihedral_angle_3_deg14.327
r_dihedral_angle_1_deg6.421
r_scangle_it5.398
r_scbond_it3.348
r_angle_other_deg2.349
r_mcangle_it2.191
r_angle_refined_deg1.789
r_mcbond_it1.219
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.288
r_dihedral_angle_4_deg23.35
r_dihedral_angle_3_deg14.327
r_dihedral_angle_1_deg6.421
r_scangle_it5.398
r_scbond_it3.348
r_angle_other_deg2.349
r_mcangle_it2.191
r_angle_refined_deg1.789
r_mcbond_it1.219
r_mcbond_other0.189
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_gen_planes_other0.006
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1349
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms17

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
ARPmodel building
Cootmodel building
CCP4model building
SHELXEmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
CCP4phasing