7H9A

Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z56899125 (CHIKV_MacB-x1410)


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
2.6854.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.974α = 90
b = 87.974β = 90
c = 85.653γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-11-21SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92124DiamondI04-1

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
11.6356.9299.90.0980.1030.0310.99911.610.692482
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)
11.631.6698.63.8424.0341.2230.34610.7

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6356.9986316470298.420.194880.192680.23785RANDOM38.418
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]
0.530.270.53-1.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.809
r_dihedral_angle_4_deg18.478
r_dihedral_angle_3_deg16.224
r_long_range_B_refined10.592
r_long_range_B_other10.507
r_dihedral_angle_1_deg6.777
r_scangle_other6.203
r_scbond_it4.096
r_scbond_other4.096
r_mcangle_it3.969
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.809
r_dihedral_angle_4_deg18.478
r_dihedral_angle_3_deg16.224
r_long_range_B_refined10.592
r_long_range_B_other10.507
r_dihedral_angle_1_deg6.777
r_scangle_other6.203
r_scbond_it4.096
r_scbond_other4.096
r_mcangle_it3.969
r_mcangle_other3.968
r_mcbond_other2.843
r_mcbond_it2.533
r_angle_refined_deg1.553
r_angle_other_deg1.315
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4962
Nucleic Acid Atoms
Solvent Atoms493
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction