5R5J

PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13964a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.0239.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.7α = 90
b = 52.23β = 90
c = 101.88γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-02SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92819DiamondI04-1

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
11.9828.4799.50.1320.1440.0560.9989.46.419034
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)
11.982.0397.91.5721.7030.650.5426.71350

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 SYNTHESISTHROUGHOUT5LF91.9828.4917940105099.290.18160.17830.2361RANDOM35.273
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]
1.78-2.330.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.016
r_dihedral_angle_4_deg16.318
r_dihedral_angle_3_deg14.261
r_dihedral_angle_1_deg6.674
r_mcangle_it3.827
r_mcbond_other2.859
r_mcbond_it2.858
r_angle_refined_deg1.622
r_angle_other_deg1.296
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.016
r_dihedral_angle_4_deg16.318
r_dihedral_angle_3_deg14.261
r_dihedral_angle_1_deg6.674
r_mcangle_it3.827
r_mcbond_other2.859
r_mcbond_it2.858
r_angle_refined_deg1.622
r_angle_other_deg1.296
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2198
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing