5QGS

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000476a


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
4.2871.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.83α = 90
b = 125.83β = 90
c = 41.53γ = 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
11.5531.4699.90.0950.1010.0320.99813.61054854
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)
11.551.5999.92.2512.3680.7330.58710.44038

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 SYNTHESISTHROUGHOUT5T3P1.55108.9752048280399.910.16570.16420.1951RANDOM32.119
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]
0.120.060.12-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.837
r_sphericity_free26.545
r_dihedral_angle_4_deg16.654
r_dihedral_angle_3_deg13.763
r_sphericity_bonded11.167
r_dihedral_angle_1_deg5.748
r_mcangle_it3.488
r_rigid_bond_restr3.329
r_mcbond_it2.819
r_mcbond_other2.784
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.837
r_sphericity_free26.545
r_dihedral_angle_4_deg16.654
r_dihedral_angle_3_deg13.763
r_sphericity_bonded11.167
r_dihedral_angle_1_deg5.748
r_mcangle_it3.488
r_rigid_bond_restr3.329
r_mcbond_it2.819
r_mcbond_other2.784
r_angle_refined_deg1.753
r_angle_other_deg0.986
r_chiral_restr0.117
r_bond_refined_d0.016
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 Atoms175
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing