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Crystal structure of macrodomain from Venezuelan equine encephalitis virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 Lithium chloride, HEPES, PEG 6000
Crystal Properties Matthews coefficient Solvent content 1.95 37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.543 α = 90 b = 98.467 β = 118.29 c = 39.514 γ = 90
Symmetry Space Group P 1 21 1
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 2023-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97857 NSLS-II 19-ID
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 1.3 50 92.1 0.149 0.163 0.066 1 11.5 5.5 60073
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 1.3 1.32 43.4 0.497 0.579 0.285 0.436 2.8
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 1.3 49.23 51833 2731 83.6 0.14853 0.14689 0.1526 0.17729 0.1793 RANDOM 15.078
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] 4.35 -1.08 -2.71 -1.65
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.249 r_dihedral_angle_3_deg 12.314 r_long_range_B_other 10.576 r_dihedral_angle_1_deg 5.833 r_scangle_other 5.301 r_mcangle_other 4.308 r_mcangle_it 4.307 r_scbond_it 3.446 r_scbond_other 3.437 r_dihedral_angle_2_deg 2.841
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.249 r_dihedral_angle_3_deg 12.314 r_long_range_B_other 10.576 r_dihedral_angle_1_deg 5.833 r_scangle_other 5.301 r_mcangle_other 4.308 r_mcangle_it 4.307 r_scbond_it 3.446 r_scbond_other 3.437 r_dihedral_angle_2_deg 2.841 r_mcbond_it 2.839 r_mcbond_other 2.832 r_rigid_bond_restr 2.557 r_angle_refined_deg 1.28 r_angle_other_deg 0.471 r_chiral_restr 0.069 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2439 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 phasing