7OMY

Thermus sp. 2.9 DarT in complex with carba-NAD+ and ssDNA


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29450 mM potassium thiocyanate, 10% (w/v) PEG2000MME
Crystal Properties
Matthews coefficientSolvent content
1.9536.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.499α = 90
b = 39.104β = 99.461
c = 61.636γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2019-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

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
11.639.1199.90.0920.1040.0470.9967.44.326615
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)
11.61.640.8030.9390.4790.6251.3

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_12921160231.637.54226597134599.8270.1640.16220.196821.741
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]
-0.819-0.653-0.2221.193
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.802
r_dihedral_angle_4_deg19.903
r_dihedral_angle_3_deg13.562
r_dihedral_angle_1_deg7.265
r_lrange_it4.291
r_lrange_other4.222
r_scangle_it2.699
r_scangle_other2.697
r_angle_refined_deg1.845
r_scbond_it1.759
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.802
r_dihedral_angle_4_deg19.903
r_dihedral_angle_3_deg13.562
r_dihedral_angle_1_deg7.265
r_lrange_it4.291
r_lrange_other4.222
r_scangle_it2.699
r_scangle_other2.697
r_angle_refined_deg1.845
r_scbond_it1.759
r_scbond_other1.756
r_mcangle_other1.652
r_mcangle_it1.651
r_angle_other_deg1.454
r_mcbond_it1.11
r_mcbond_other1.106
r_symmetry_xyhbond_nbd_refined0.204
r_nbd_other0.203
r_nbd_refined0.197
r_symmetry_nbd_other0.19
r_nbtor_refined0.185
r_symmetry_nbd_refined0.139
r_xyhbond_nbd_refined0.127
r_chiral_restr0.097
r_symmetry_nbtor_other0.084
r_bond_refined_d0.013
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 Atoms99
Solvent Atoms151
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing