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Crystal structure of O'nyong'nyong virus capsid protease (106-256)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.1 M sodium cacodylate (pH 6.5), 2.2 M ammonium sulfate and 100 mM ethylenediaminetetraacetic acid disodium salt
Crystals were cryoprotected in 25% (v/v) glycerol in the reservoir solution and flash-cooled in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.54 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.65 α = 90 b = 112.13 β = 89.97 c = 67.1 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2022-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 48.46 98.9 0.961 2.5 1.7 51622
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 0.157 0.6
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 1.9 44.865 51597 2100 98.868 0.227 0.2253 0.2253 0.268 0.2679 42.13
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] -3.036 0.52 -1.658 4.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.445 r_dihedral_angle_3_deg 15.509 r_dihedral_angle_2_deg 12.157 r_lrange_it 11.721 r_lrange_other 11.593 r_scangle_it 8.667 r_scangle_other 8.427 r_dihedral_angle_1_deg 8.186 r_mcangle_other 5.987 r_mcangle_it 5.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.445 r_dihedral_angle_3_deg 15.509 r_dihedral_angle_2_deg 12.157 r_lrange_it 11.721 r_lrange_other 11.593 r_scangle_it 8.667 r_scangle_other 8.427 r_dihedral_angle_1_deg 8.186 r_mcangle_other 5.987 r_mcangle_it 5.986 r_scbond_it 5.63 r_scbond_other 5.431 r_mcbond_it 4.069 r_mcbond_other 4.046 r_angle_refined_deg 1.588 r_angle_other_deg 0.609 r_xyhbond_nbd_refined 0.181 r_nbd_refined 0.163 r_symmetry_nbd_other 0.161 r_nbtor_refined 0.161 r_ncsr_local_group_3 0.15 r_ncsr_local_group_5 0.149 r_nbd_other 0.141 r_ncsr_local_group_2 0.129 r_ncsr_local_group_4 0.126 r_ncsr_local_group_6 0.125 r_symmetry_nbd_refined 0.108 r_symmetry_xyhbond_nbd_refined 0.093 r_ncsr_local_group_1 0.08 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4514 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing