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Crystal structure of Mayaro virus capsid C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VCP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 22% PEG 3350, 100mM Bis-Tris pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.39 48.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.16 α = 93.585 b = 40.112 β = 94.403 c = 56.511 γ = 111.925
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 PILATUS 2M 2021-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS SIRIUS BEAMLINE MANACA 0.9772 LNLS SIRIUS MANACA
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 1.18 37.057 93.08 0.05812 0.06895 0.03665 0.994 16.96 3.6 96920 9.59
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 1.18 1.222 0.09189 0.1084 0.05683 0.988 10.72
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.18 37.057 96920 4894 93.087 0.166 0.1648 0.1734 0.1806 0.19 13.381
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] 0.459 -0.115 0.046 -0.15 -0.048 -0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.195 r_lrange_other 16.364 r_lrange_it 16.096 r_dihedral_angle_4_deg 15.888 r_scangle_it 11.855 r_scangle_other 11.851 r_mcangle_it 11.613 r_mcangle_other 11.611 r_dihedral_angle_3_deg 9.248 r_scbond_it 9.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.195 r_lrange_other 16.364 r_lrange_it 16.096 r_dihedral_angle_4_deg 15.888 r_scangle_it 11.855 r_scangle_other 11.851 r_mcangle_it 11.613 r_mcangle_other 11.611 r_dihedral_angle_3_deg 9.248 r_scbond_it 9.002 r_scbond_other 8.999 r_dihedral_angle_1_deg 7.459 r_mcbond_it 7.402 r_mcbond_other 7.4 r_angle_refined_deg 1.786 r_angle_other_deg 1.747 r_nbd_refined 0.224 r_symmetry_nbd_other 0.211 r_nbd_other 0.19 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.156 r_xyhbond_nbd_refined 0.128 r_symmetry_xyhbond_nbd_refined 0.118 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.082 r_gen_planes_other 0.032 r_bond_other_d 0.018 r_bond_refined_d 0.016 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2286 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 32
Software Software Software Name Purpose MxCuBE data collection XDS data reduction SCALA data scaling BALBES phasing REFMAC refinement PDB-REDO refinement