5QK8

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1271660837


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
2.4249.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.27α = 79.55
b = 59.91β = 81.38
c = 80.011γ = 75.74
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-29SINGLE 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
11.7141.4295.40.0260.0360.0260.99911.71.789368
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)
11.711.7594.20.4160.5880.4160.8111.66536

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 SYNTHESISTHROUGHOUT6GRU1.7178.284830449995.150.22690.22510.26RANDOM34.624
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]
3.291.41-0.17-1.250.9-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.97
r_dihedral_angle_3_deg15.113
r_dihedral_angle_4_deg14.353
r_dihedral_angle_1_deg7.257
r_mcangle_it4.218
r_mcbond_it3.097
r_mcbond_other3.097
r_angle_refined_deg1.981
r_angle_other_deg1.047
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.97
r_dihedral_angle_3_deg15.113
r_dihedral_angle_4_deg14.353
r_dihedral_angle_1_deg7.257
r_mcangle_it4.218
r_mcbond_it3.097
r_mcbond_other3.097
r_angle_refined_deg1.981
r_angle_other_deg1.047
r_chiral_restr0.122
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5709
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing