7H97

Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z276614452 (CHIKV_MacB-x1397)


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
2.6753.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.625α = 90
b = 87.625β = 90
c = 85.737γ = 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
11.5475.8499.90.10.1050.0320.99911.410.3108967
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)
11.541.5797.43.5513.7831.2950.3088.4

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 REPLACEMENTTHROUGHOUT1.5475.89101069545797.760.186810.18520.21779RANDOM31.666
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]
0.320.160.32-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.515
r_dihedral_angle_4_deg20.143
r_dihedral_angle_3_deg15.395
r_long_range_B_refined7.38
r_long_range_B_other7.272
r_dihedral_angle_1_deg6.069
r_scangle_other4.93
r_scbond_it3.168
r_scbond_other3.168
r_mcangle_it2.825
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.515
r_dihedral_angle_4_deg20.143
r_dihedral_angle_3_deg15.395
r_long_range_B_refined7.38
r_long_range_B_other7.272
r_dihedral_angle_1_deg6.069
r_scangle_other4.93
r_scbond_it3.168
r_scbond_other3.168
r_mcangle_it2.825
r_mcangle_other2.825
r_mcbond_other2.045
r_mcbond_it1.887
r_angle_refined_deg1.494
r_angle_other_deg1.32
r_chiral_restr0.076
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 Atoms580
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction