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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 Z1041785508 (CHIKV_MacB-x0281)
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 53.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.374 α = 90 b = 87.374 β = 90 c = 85.505 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 2023-10-05 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 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 1.33 85.51 99.8 0.057 0.06 0.019 0.999 16.5 8.9 167465
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 1.33 1.35 96.4 1.447 1.693 0.856 0.351 3.8
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 1.33 75.67 158417 8227 99.3 0.17795 0.17679 0.1995 0.20054 0.2207 RANDOM 24.774
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] -0.05 -0.02 -0.05 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.303 r_dihedral_angle_4_deg 21.216 r_dihedral_angle_3_deg 15.137 r_long_range_B_other 6.469 r_long_range_B_refined 6.468 r_dihedral_angle_1_deg 5.748 r_scangle_other 4.085 r_scbond_it 2.427 r_scbond_other 2.427 r_mcangle_it 2.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.303 r_dihedral_angle_4_deg 21.216 r_dihedral_angle_3_deg 15.137 r_long_range_B_other 6.469 r_long_range_B_refined 6.468 r_dihedral_angle_1_deg 5.748 r_scangle_other 4.085 r_scbond_it 2.427 r_scbond_other 2.427 r_mcangle_it 2.307 r_mcangle_other 2.307 r_angle_refined_deg 1.677 r_mcbond_other 1.408 r_angle_other_deg 1.391 r_mcbond_it 1.358 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 705 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction