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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 Z728187792 (CHIKV_MacB-x1423)
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 2.67 53.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.68 α = 90 b = 87.68 β = 90 c = 85.62 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 2023-11-24 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 1.53 56.81 100 0.109 0.114 0.035 0.999 9.2 10.3 111118
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 1.53 1.56 100 3.017 3.221 1.11 0.317 8.3
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 1.53 56.87 98136 5299 93.14 0.20198 0.20016 0.2225 0.23729 0.2503 RANDOM 32.832
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] 0.41 0.21 0.41 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.517 r_dihedral_angle_4_deg 20.547 r_dihedral_angle_3_deg 15.958 r_long_range_B_refined 8.463 r_long_range_B_other 8.463 r_dihedral_angle_1_deg 6.436 r_scangle_other 4.839 r_mcangle_other 3.045 r_mcangle_it 3.044 r_scbond_other 2.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.517 r_dihedral_angle_4_deg 20.547 r_dihedral_angle_3_deg 15.958 r_long_range_B_refined 8.463 r_long_range_B_other 8.463 r_dihedral_angle_1_deg 6.436 r_scangle_other 4.839 r_mcangle_other 3.045 r_mcangle_it 3.044 r_scbond_other 2.974 r_scbond_it 2.973 r_mcbond_it 1.896 r_mcbond_other 1.895 r_angle_refined_deg 1.487 r_angle_other_deg 1.302 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 599 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement REFMAC5 refinement Aimless data scaling PHASER phasing XDS data reduction