5QJH

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z375990520


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
2.3948.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.01α = 79.41
b = 59.63β = 81.64
c = 79.83γ = 75.79
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-08SINGLE 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
12.0343.0396.20.0760.1080.0760.9971.853231
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)
12.032.0894.80.5220.7390.5220.7461.73867

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 SYNTHESISTHROUGHOUT6GRU2.0378.0350594263696.150.22610.22370.2727RANDOM39.869
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]
3.70.480.91-0.480.76-2.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.856
r_dihedral_angle_4_deg16.273
r_dihedral_angle_3_deg15.333
r_dihedral_angle_1_deg7.312
r_mcangle_it4.428
r_mcbond_other2.933
r_mcbond_it2.932
r_angle_refined_deg1.665
r_angle_other_deg0.956
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.856
r_dihedral_angle_4_deg16.273
r_dihedral_angle_3_deg15.333
r_dihedral_angle_1_deg7.312
r_mcangle_it4.428
r_mcbond_other2.933
r_mcbond_it2.932
r_angle_refined_deg1.665
r_angle_other_deg0.956
r_chiral_restr0.09
r_bond_refined_d0.014
r_gen_planes_refined0.008
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 Atoms225
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing