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Crystal Structure of Human Parechovirus 1 2A protein lacking the C-terminal oligomerisation helix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZU3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 15% PEG 8000
0.5 M lithium sulphate
Crystal Properties Matthews coefficient Solvent content 2.98 58.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.425 α = 90 b = 76.425 β = 90 c = 121.724 γ = 90
Symmetry Space Group P 43 21 2
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 6M 2014-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976250 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 49.39 100 0.09 0.047 0.999 15.9 8.6 21802
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 1.209 0.618 0.624
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 7ZU3 2.1 49.39 21743 1082 99.982 0.199 0.1976 0.2031 0.2202 0.2225 50.814
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] 0.412 0.412 -0.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.668 r_dihedral_angle_3_deg 12.163 r_lrange_it 11.752 r_lrange_other 11.751 r_scangle_it 10.441 r_scangle_other 10.437 r_scbond_it 8.599 r_scbond_other 8.599 r_dihedral_angle_2_deg 8.213 r_mcangle_it 6.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.668 r_dihedral_angle_3_deg 12.163 r_lrange_it 11.752 r_lrange_other 11.751 r_scangle_it 10.441 r_scangle_other 10.437 r_scbond_it 8.599 r_scbond_other 8.599 r_dihedral_angle_2_deg 8.213 r_mcangle_it 6.893 r_mcangle_other 6.891 r_dihedral_angle_1_deg 5.978 r_mcbond_it 5.035 r_mcbond_other 5.025 r_angle_refined_deg 0.9 r_angle_other_deg 0.322 r_symmetry_nbd_refined 0.206 r_nbd_refined 0.2 r_symmetry_xyhbond_nbd_refined 0.199 r_nbtor_refined 0.176 r_symmetry_nbd_other 0.17 r_ncsr_local_group_1 0.165 r_nbd_other 0.156 r_xyhbond_nbd_refined 0.11 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1920 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing