7H7C | pdb_00007h7c

Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z31504642 (CHIKV_MacB-x0692)


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
2.6353.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.135α = 90
b = 87.135β = 90
c = 85.563γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2023-11-23SINGLE 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
11.3956.61000.0710.0740.0230.99914.69.5146124
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)
11.391.4199.92.3852.5981.0220.3476.3

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 REPLACEMENTTHROUGHOUT1.3956.66138264723199.560.177920.176640.20.202610.22RANDOM27.808
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]
0.250.120.25-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.117
r_dihedral_angle_4_deg18.885
r_dihedral_angle_3_deg15.68
r_long_range_B_refined7.363
r_long_range_B_other7.263
r_dihedral_angle_1_deg6.139
r_scangle_other4.338
r_scbond_it2.692
r_scbond_other2.692
r_mcangle_it2.642
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.117
r_dihedral_angle_4_deg18.885
r_dihedral_angle_3_deg15.68
r_long_range_B_refined7.363
r_long_range_B_other7.263
r_dihedral_angle_1_deg6.139
r_scangle_other4.338
r_scbond_it2.692
r_scbond_other2.692
r_mcangle_it2.642
r_mcangle_other2.641
r_mcbond_other1.709
r_angle_refined_deg1.613
r_mcbond_it1.572
r_angle_other_deg1.367
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_gen_planes_other0.003
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 Atoms627
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction