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Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z57127349 (CHIKV_MacB-x1112)
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 2.62 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.228 α = 90 b = 87.228 β = 90 c = 85.159 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 2023-11-19 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 Diamond I03
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 1.78 56.51 99.8 0.189 0.199 0.061 0.993 5.7 10.5 69271
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 1.78 1.82 98.2 2.821 2.969 0.921 0.374 10.4
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 1.78 56.58 65408 3528 99.41 0.19562 0.19314 0.2295 0.24442 0.2666 RANDOM 36.499
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] 0.35 0.17 0.35 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.536 r_dihedral_angle_4_deg 19.084 r_dihedral_angle_3_deg 16.003 r_long_range_B_refined 8.117 r_long_range_B_other 7.966 r_dihedral_angle_1_deg 6.255 r_scangle_other 3.988 r_mcangle_other 2.827 r_mcangle_it 2.826 r_scbond_it 2.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.536 r_dihedral_angle_4_deg 19.084 r_dihedral_angle_3_deg 16.003 r_long_range_B_refined 8.117 r_long_range_B_other 7.966 r_dihedral_angle_1_deg 6.255 r_scangle_other 3.988 r_mcangle_other 2.827 r_mcangle_it 2.826 r_scbond_it 2.319 r_scbond_other 2.319 r_mcbond_other 1.749 r_mcbond_it 1.716 r_angle_refined_deg 1.359 r_angle_other_deg 1.255 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 527 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction