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Ty1 Prime Retrotransposon Capsid C-Terminal Domain, F323S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Related entry (Ty1 Prime Retrotransposon Capsid C-Terminal Domain, wt) was used as a search model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 150 nL protein (70mg/ml (6.33mM) in 20 mM Tris pH 8.5, 150mM NaCl, 1mM TCEP) mixed with 50 nL well solution (0.2M NH4Cl, 20% PEG6K, 0.1M Tris pH8)
Crystal Properties Matthews coefficient Solvent content 1.88 34.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.232 α = 90 b = 52.753 β = 108.538 c = 45.959 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2021-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.99990 Diamond I24
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 1.616 43.58 71.4 0.087 0.03 0.997 10.81 7.8 15110 38.49
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 1.616 1.789 13.61 1.073 0.465 0.5964
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 1.616 43.575 15109 759 71.383 0.224 0.2221 0.2288 0.2682 0.2771 Random selection 36.031
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] 1.126 0.263 -1.735 0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.054 r_dihedral_angle_3_deg 15.367 r_dihedral_angle_6_deg 13.976 r_lrange_it 6.397 r_lrange_other 6.389 r_scangle_it 4.856 r_scangle_other 4.854 r_dihedral_angle_1_deg 4.568 r_mcangle_other 3.774 r_mcangle_it 3.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.054 r_dihedral_angle_3_deg 15.367 r_dihedral_angle_6_deg 13.976 r_lrange_it 6.397 r_lrange_other 6.389 r_scangle_it 4.856 r_scangle_other 4.854 r_dihedral_angle_1_deg 4.568 r_mcangle_other 3.774 r_mcangle_it 3.773 r_scbond_it 3.131 r_scbond_other 3.129 r_mcbond_it 2.397 r_mcbond_other 2.394 r_angle_refined_deg 1.262 r_angle_other_deg 0.398 r_nbd_other 0.345 r_symmetry_nbd_refined 0.309 r_nbd_refined 0.238 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.133 r_symmetry_xyhbond_nbd_refined 0.128 r_ncsr_local_group_1 0.086 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1379 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing BUCCANEER model building Coot model building REFMAC refinement