5QJX

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z2856434778


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
2.3948.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.52α = 79.68
b = 59.52β = 82.36
c = 80.62γ = 76.36
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-28SINGLE 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
11.7357.1696.40.0510.0720.0510.9938.91.886383
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)
11.731.7795.80.6230.8820.6230.6991.86385

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 SYNTHESISTHROUGHOUT6GRU1.7378.9682072431096.310.22220.22040.2564RANDOM37.89
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]
3.410.41.83-0.621.61-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.486
r_dihedral_angle_4_deg15.859
r_dihedral_angle_3_deg14.232
r_dihedral_angle_1_deg7.085
r_mcangle_it4.875
r_mcbond_other3.631
r_mcbond_it3.63
r_angle_refined_deg1.89
r_angle_other_deg1.03
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.486
r_dihedral_angle_4_deg15.859
r_dihedral_angle_3_deg14.232
r_dihedral_angle_1_deg7.085
r_mcangle_it4.875
r_mcbond_other3.631
r_mcbond_it3.63
r_angle_refined_deg1.89
r_angle_other_deg1.03
r_chiral_restr0.114
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5713
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing