5QP7

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with PB1230873739


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52770.1 M acetate, pH 4.5, 5-25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.550.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.365α = 90
b = 60.452β = 90
c = 65.353γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayPIXELDECTRIS PILATUS 2M2017-07-27SINGLE 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
11.8828.7599.30.0530.0580.0230.99919.56.516044
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)
11.881.9397.80.660.7150.2720.9186.71152

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 SYNTHESISTHROUGHOUTPDB entry 5MP01.8844.421521177198.90.19950.19660.2597RANDOM35.979
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]
1.71-2.250.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.358
r_dihedral_angle_4_deg23.877
r_dihedral_angle_3_deg16.436
r_dihedral_angle_1_deg5.808
r_mcangle_it4.321
r_mcbond_it2.964
r_mcbond_other2.932
r_angle_refined_deg1.829
r_angle_other_deg1.03
r_chiral_restr0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.358
r_dihedral_angle_4_deg23.877
r_dihedral_angle_3_deg16.436
r_dihedral_angle_1_deg5.808
r_mcangle_it4.321
r_mcbond_it2.964
r_mcbond_other2.932
r_angle_refined_deg1.829
r_angle_other_deg1.03
r_chiral_restr0.11
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1189
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing