7OMW

Thermus sp. 2.9 DarT in complex with NAD+


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, 20% (w/v) PEG2000MME
Crystal Properties
Matthews coefficientSolvent content
2.2845.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.032α = 90
b = 61.745β = 95.198
c = 50.197γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.335.909970.0410.0450.0170.99920.35.952232
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)
11.31.320.2270.2770.1550.9493.5

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-VALUED_12921160231.335.90952208251896.8990.1320.1310.152517.786
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]
1.524-2.648-0.37-0.662
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.894
r_dihedral_angle_4_deg19
r_dihedral_angle_3_deg13.326
r_rigid_bond_restr7.617
r_dihedral_angle_1_deg6.76
r_lrange_it4.176
r_scangle_it3.827
r_lrange_other3.817
r_scangle_other3.811
r_scbond_it3.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.894
r_dihedral_angle_4_deg19
r_dihedral_angle_3_deg13.326
r_rigid_bond_restr7.617
r_dihedral_angle_1_deg6.76
r_lrange_it4.176
r_scangle_it3.827
r_lrange_other3.817
r_scangle_other3.811
r_scbond_it3.083
r_scbond_other3.039
r_mcangle_it2.221
r_mcangle_other2.22
r_mcbond_it1.817
r_mcbond_other1.816
r_angle_refined_deg1.803
r_angle_other_deg1.45
r_symmetry_nbd_refined0.353
r_nbd_refined0.273
r_symmetry_xyhbond_nbd_refined0.272
r_nbd_other0.221
r_symmetry_nbd_other0.188
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.127
r_chiral_restr0.105
r_symmetry_nbtor_other0.086
r_symmetry_xyhbond_nbd_other0.024
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1627
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing