6W0T

Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6VUQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629121-24% PEG 400, 0.1 M sodium citrate pH5.6, 10% isopropanol
Crystal Properties
Matthews coefficientSolvent content
2.550.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.774α = 90
b = 87.774β = 90
c = 83.105γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2018-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.9576.2898.60.06114.25.352180
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9520.514

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6VUQ1.9576.0148724270098.550.22980.22830.2575RANDOM47.018
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]
-0.51-0.26-0.511.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.757
r_dihedral_angle_4_deg19.334
r_dihedral_angle_3_deg12.985
r_dihedral_angle_1_deg5.499
r_angle_refined_deg1.142
r_angle_other_deg0.89
r_chiral_restr0.059
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.757
r_dihedral_angle_4_deg19.334
r_dihedral_angle_3_deg12.985
r_dihedral_angle_1_deg5.499
r_angle_refined_deg1.142
r_angle_other_deg0.89
r_chiral_restr0.059
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4903
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction