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Structure of Human Parainfluenza Virus 3 Unassembled Nucleoprotein in Complex with its viral chaperone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 PEG 6000, Cacodylate, Nickel chloride
Crystal Properties Matthews coefficient Solvent content 2.81 56.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.09 α = 90 b = 117.09 β = 90 c = 143.177 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2020-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.23 50 99.8 0.098 0.106 0.04 9.1 6.8 8248
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 3.23 3.29 99.5 0.901 1 0.422 0.686 5.3
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6H5Q 3.234 49.178 8015 385 96.823 0.22 0.2192 0.2056 0.2378 0.221 RANDOM 45.392
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] 3.885 3.885 -7.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.802 r_dihedral_angle_4_deg 18.184 r_dihedral_angle_3_deg 17.88 r_lrange_it 10.467 r_lrange_other 10.438 r_mcangle_it 6.02 r_mcangle_other 6.02 r_scangle_other 5.532 r_scangle_it 5.531 r_dihedral_angle_1_deg 5.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.802 r_dihedral_angle_4_deg 18.184 r_dihedral_angle_3_deg 17.88 r_lrange_it 10.467 r_lrange_other 10.438 r_mcangle_it 6.02 r_mcangle_other 6.02 r_scangle_other 5.532 r_scangle_it 5.531 r_dihedral_angle_1_deg 5.026 r_mcbond_it 3.612 r_mcbond_other 3.579 r_scbond_it 3.377 r_scbond_other 3.376 r_angle_other_deg 1.47 r_angle_refined_deg 1.411 r_symmetry_nbd_refined 0.315 r_nbd_refined 0.214 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.174 r_nbd_other 0.167 r_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_refined 0.103 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_ext_dist_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2654 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing