5QGT

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000609a


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Crystal Properties
Matthews coefficientSolvent content
4.3671.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.781α = 90
b = 126.781β = 90
c = 41.762γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-05-11SINGLE 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
11.9729.4499.60.0740.0790.0250.99921.39.927194
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)
11.972.0395.20.9470.9980.3120.8249.81897

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 SYNTHESISTHROUGHOUT5T3P1.97109.825722144899.510.19030.1890.2139RANDOM42.198
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]
0.560.280.56-1.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.301
r_dihedral_angle_4_deg21.742
r_dihedral_angle_3_deg14.061
r_dihedral_angle_1_deg6.195
r_mcangle_it4.516
r_mcbond_it3.248
r_mcbond_other3.228
r_angle_refined_deg1.798
r_angle_other_deg1.001
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.301
r_dihedral_angle_4_deg21.742
r_dihedral_angle_3_deg14.061
r_dihedral_angle_1_deg6.195
r_mcangle_it4.516
r_mcbond_it3.248
r_mcbond_other3.228
r_angle_refined_deg1.798
r_angle_other_deg1.001
r_chiral_restr0.115
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1467
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing