7OMU

Thermosipho africanus DarTG in complex with ADP-ribose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M31 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2940.2 M potassium thiocyanate, 0.1 M TRIS pH 7.5, 8% (w/v) PEG 20,000, 8% (v/v) PEG500MME
Crystal Properties
Matthews coefficientSolvent content
2.9458.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 187.458α = 90
b = 187.458β = 90
c = 187.458γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.9693.731000.0740.0780.024117.310.722975
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.963.041.7131.7990.5450.5331.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5M312.9676.64722813114299.4550.2130.21070.2482102.859
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.398
r_dihedral_angle_3_deg16.951
r_dihedral_angle_4_deg16.171
r_lrange_it7.806
r_lrange_other7.805
r_dihedral_angle_1_deg6.652
r_mcangle_it4.684
r_mcangle_other4.684
r_scangle_it4.337
r_scangle_other4.337
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.398
r_dihedral_angle_3_deg16.951
r_dihedral_angle_4_deg16.171
r_lrange_it7.806
r_lrange_other7.805
r_dihedral_angle_1_deg6.652
r_mcangle_it4.684
r_mcangle_other4.684
r_scangle_it4.337
r_scangle_other4.337
r_mcbond_it2.698
r_mcbond_other2.696
r_scbond_it2.447
r_scbond_other2.447
r_angle_refined_deg1.244
r_angle_other_deg1.053
r_symmetry_xyhbond_nbd_refined0.269
r_nbd_refined0.179
r_nbd_other0.179
r_symmetry_nbd_other0.17
r_nbtor_refined0.158
r_symmetry_nbd_refined0.139
r_xyhbond_nbd_refined0.099
r_symmetry_nbtor_other0.074
r_ncsr_local_group_10.06
r_chiral_restr0.046
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6122
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing