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Ty1 Prime Retrotransposon Capsid C-Terminal Domain, wt
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NLH Polyalanine model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 150 nL protein (12 mg/ml (1.067mM) in 20 mM Tris pH 8.5, 150mM NaCl, 1mM TCEP) mixed with 50 nL well solution (0.2M NaCl, 10% PEG3K, 0.1M Na Phos Citrate pH4.2)
Crystal Properties Matthews coefficient Solvent content 2 38.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.593 α = 101.641 b = 34.332 β = 96.351 c = 45.333 γ = 109.279
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 16M 2020-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 43.59 82.6 0.067 0.034 0.999 20 3.4 18863 20.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 31.26 1.524 0.833 0.492 3.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 43.577 18833 978 82.496 0.181 0.1798 0.1902 0.2022 0.2099 Random selection 23.523
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] 0.695 -0.722 -1.663 0.886 -0.925 0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.37 r_dihedral_angle_6_deg 14.9 r_dihedral_angle_3_deg 14.425 r_lrange_it 6.442 r_lrange_other 6.411 r_dihedral_angle_1_deg 4.987 r_scangle_it 4.082 r_scangle_other 4.08 r_mcangle_other 2.929 r_mcangle_it 2.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.37 r_dihedral_angle_6_deg 14.9 r_dihedral_angle_3_deg 14.425 r_lrange_it 6.442 r_lrange_other 6.411 r_dihedral_angle_1_deg 4.987 r_scangle_it 4.082 r_scangle_other 4.08 r_mcangle_other 2.929 r_mcangle_it 2.928 r_scbond_it 2.759 r_scbond_other 2.757 r_mcbond_it 1.786 r_mcbond_other 1.785 r_angle_refined_deg 1.375 r_angle_other_deg 0.489 r_symmetry_xyhbond_nbd_other 0.254 r_nbd_refined 0.239 r_symmetry_nbd_other 0.194 r_symmetry_nbd_refined 0.192 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.141 r_nbd_other 0.138 r_ncsr_local_group_1 0.099 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_refined 0.041 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1417 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose xia2 data reduction DIALS data reduction TRUNCATE data scaling PHASER phasing ARP/wARP model building Coot model building REFMAC refinement