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Group deposition for combi-soaks of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z1041785508 and Z1267773765 (CHIKV_MacB-x1483)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293.15 0.1 M Potassium thiocyanate, 0.1 M Sodium bromide, 0.1 M Tris, pH 7.8, 25 % PEG Smear Broad
Crystal Properties Matthews coefficient Solvent content 2.64 53.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.349 α = 90 b = 87.349 β = 90 c = 85.513 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 9M 2024-04-19 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92208 Diamond I04-1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.68 85.51 100 0.116 0.122 0.037 0.998 10.1 10.6 83196
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) Redundancy Number Unique Reflections (All) 1 1.68 1.71 100 3.229 3.393 1.04 0.392 10.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.68 75.65 78806 4262 99.86 0.1795 0.17764 0.2259 0.21612 0.253 RANDOM 32.947
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] 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.512 r_dihedral_angle_4_deg 19.299 r_dihedral_angle_3_deg 14.918 r_long_range_B_refined 7.841 r_long_range_B_other 7.739 r_dihedral_angle_1_deg 6.275 r_scangle_other 4.644 r_mcangle_it 2.816 r_mcangle_other 2.816 r_scbond_it 2.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.512 r_dihedral_angle_4_deg 19.299 r_dihedral_angle_3_deg 14.918 r_long_range_B_refined 7.841 r_long_range_B_other 7.739 r_dihedral_angle_1_deg 6.275 r_scangle_other 4.644 r_mcangle_it 2.816 r_mcangle_other 2.816 r_scbond_it 2.577 r_scbond_other 2.577 r_mcbond_other 1.666 r_mcbond_it 1.559 r_angle_refined_deg 1.406 r_angle_other_deg 1.295 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 4962 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction