5QJ6

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1614545742


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1533 % PEG4k, 0.2 MgCl2 and 0.1 M Tris
Crystal Properties
Matthews coefficientSolvent content
2.4149.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.25α = 79.42
b = 59.78β = 81.68
c = 80.09γ = 75.64
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-07SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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
11.6531.8796.30.0380.0530.0380.99710.11.8100263
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)
11.651.6994.80.5820.8240.5820.7191.67347

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6GRU1.6578.395204505996.220.21350.21170.249RANDOM33.707
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]
2.961.180.25-0.550.89-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.525
r_dihedral_angle_3_deg14.545
r_dihedral_angle_4_deg11.302
r_dihedral_angle_1_deg7.177
r_mcangle_it4.264
r_mcbond_other3.119
r_mcbond_it3.097
r_angle_refined_deg1.951
r_angle_other_deg1.05
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.525
r_dihedral_angle_3_deg14.545
r_dihedral_angle_4_deg11.302
r_dihedral_angle_1_deg7.177
r_mcangle_it4.264
r_mcbond_other3.119
r_mcbond_it3.097
r_angle_refined_deg1.951
r_angle_other_deg1.05
r_chiral_restr0.115
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5715
Nucleic Acid Atoms
Solvent Atoms261
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing