7OMZ

Thermus sp. 2.9 DarT in complex with ADP-ribosylated ssDNA and nicotinamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7OMVD_1292116023

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294150 mM potassium thiocyanate, 10% (w/v) PEG2000MME
Crystal Properties
Matthews coefficientSolvent content
1.8834.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.963α = 90
b = 38.89β = 101.805
c = 61.179γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.8998DiamondI24

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
11.6638.8998.10.1340.1490.0630.9926.65.322671
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)
11.661.6980.70.6220.7210.3560.7221.63.7

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-VALUED_12921160231.6637.68522657107698.0230.1530.15120.180517.738
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]
-1.0270.2690.8660.045
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.347
r_dihedral_angle_4_deg23.795
r_dihedral_angle_3_deg12.32
r_dihedral_angle_1_deg7.275
r_lrange_it4.859
r_lrange_other4.638
r_scangle_it2.732
r_scangle_other2.731
r_angle_refined_deg1.847
r_scbond_it1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.347
r_dihedral_angle_4_deg23.795
r_dihedral_angle_3_deg12.32
r_dihedral_angle_1_deg7.275
r_lrange_it4.859
r_lrange_other4.638
r_scangle_it2.732
r_scangle_other2.731
r_angle_refined_deg1.847
r_scbond_it1.71
r_scbond_other1.71
r_mcangle_it1.585
r_mcangle_other1.585
r_angle_other_deg1.405
r_mcbond_it1.055
r_mcbond_other1.051
r_nbd_refined0.236
r_symmetry_nbd_other0.194
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.168
r_nbd_other0.167
r_symmetry_xyhbond_nbd_refined0.161
r_chiral_restr0.103
r_symmetry_nbtor_other0.083
r_symmetry_nbd_refined0.066
r_gen_planes_refined0.014
r_bond_refined_d0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1724
Nucleic Acid Atoms99
Solvent Atoms202
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing