5QPA

PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with FMOPL000449a


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
2.5451.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.64α = 90
b = 60.49β = 90
c = 65.77γ = 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
11.6124.32990.0360.0390.0160.99920.26.125556
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)
11.611.65991.1861.3220.5790.7245.21856

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 5MP01.6144.5624245125498.890.20970.20750.256RANDOM43.501
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]
3.1-2.66-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.917
r_dihedral_angle_4_deg18.344
r_dihedral_angle_3_deg15.917
r_dihedral_angle_1_deg6.166
r_mcangle_it5.837
r_mcbond_other3.778
r_mcbond_it3.777
r_angle_refined_deg1.928
r_angle_other_deg1.083
r_chiral_restr0.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.917
r_dihedral_angle_4_deg18.344
r_dihedral_angle_3_deg15.917
r_dihedral_angle_1_deg6.166
r_mcangle_it5.837
r_mcbond_other3.778
r_mcbond_it3.777
r_angle_refined_deg1.928
r_angle_other_deg1.083
r_chiral_restr0.125
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 Atoms1195
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing