7ON0

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294123 mM potassium thiocyanate, 12% (w/v) PEG2000MME
Crystal Properties
Matthews coefficientSolvent content
1.8734.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.889α = 90
b = 38.683β = 101.756
c = 61.012γ = 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
11.4638.681000.1320.1440.0570.9957.46.433508
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)
11.461.4999.91.3071.4520.6230.5131.15.3

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_12921160231.4632.4933491162299.9580.1640.16220.190316.031
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]
-0.394-0.3980.3770.169
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.305
r_dihedral_angle_4_deg22.105
r_dihedral_angle_3_deg13.038
r_dihedral_angle_1_deg7.026
r_lrange_it4.484
r_lrange_other4.353
r_scangle_it2.397
r_scangle_other2.396
r_angle_refined_deg1.909
r_scbond_it1.592
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.305
r_dihedral_angle_4_deg22.105
r_dihedral_angle_3_deg13.038
r_dihedral_angle_1_deg7.026
r_lrange_it4.484
r_lrange_other4.353
r_scangle_it2.397
r_scangle_other2.396
r_angle_refined_deg1.909
r_scbond_it1.592
r_scbond_other1.591
r_angle_other_deg1.477
r_mcangle_it1.374
r_mcangle_other1.374
r_mcbond_it0.913
r_mcbond_other0.912
r_symmetry_nbd_refined0.324
r_symmetry_xyhbond_nbd_refined0.242
r_nbd_refined0.241
r_nbd_other0.241
r_symmetry_nbd_other0.198
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.138
r_chiral_restr0.095
r_symmetry_nbtor_other0.085
r_bond_refined_d0.014
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1724
Nucleic Acid Atoms98
Solvent Atoms226
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing