7H83 | pdb_00007h83

Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z1741982125 (CHIKV_MacB-x1118)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.8293.150.1 M Potassium thiocyanate, 0.1 M Sodium bromide, 0.1 M Tris, pH 7.8, 25 % PEG Smear Broad
Crystal Properties
Matthews coefficientSolvent content
2.6353.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.214α = 90
b = 87.214β = 90
c = 85.328γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-11-19SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97626DiamondI03

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
11.4556.5598.80.080.0840.0260.99616.910127042
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)
11.451.4887.32.3482.581.0450.3145.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4556.62120095631598.280.17340.172080.20.198970.22RANDOM26.319
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]
0.230.120.23-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.963
r_dihedral_angle_4_deg17.987
r_dihedral_angle_3_deg15.564
r_long_range_B_other7.159
r_long_range_B_refined7.157
r_dihedral_angle_1_deg6.119
r_scangle_other4.278
r_scbond_it2.618
r_scbond_other2.618
r_mcangle_it2.384
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4962
Nucleic Acid Atoms
Solvent Atoms733
Heterogen Atoms110

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction