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S. cerevisiae Ty1 p22 restriction factor, Gag CA-CTD, AUG1 variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Ty1 p22 Aug2 variant partial model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 300 nl protein (6.25 mg mL-1, in 20 mM Tris-HCl pH 8.5, 150 mM NaCl, 1 mM TCEP)
100 nl Mother Liquor (1.16 M Li2SO4, 0.1 M Tris-HCl pH 9.0)
pH screened 7.5-9.0, Li2SO4 screened 1.125M-1.25M.
Crystal Properties Matthews coefficient Solvent content 6.07 79.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 282.124 α = 90 b = 282.124 β = 90 c = 39.967 γ = 120
Symmetry Space Group P 65 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 100 PIXEL DECTRIS EIGER2 XE 16M 2019-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97954 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 2.8 244.4 100 0.101 0.016 1 21.6 38.7 23876
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 2.8 2.95 100 3.912 0.627 0.491 1.2 38.6
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 (Observed) 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 Ty1 p22 Aug2 variant partial model 2.8 141.46 22603 1259 99.99 0.2568 0.2564 0.2481 0.2639 0.2602 RANDOM 145.564
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] 3.85 1.92 3.85 -12.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.347 r_dihedral_angle_3_deg 17.331 r_dihedral_angle_4_deg 12.969 r_dihedral_angle_1_deg 6.374 r_angle_refined_deg 1.287 r_angle_other_deg 1.181 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.347 r_dihedral_angle_3_deg 17.331 r_dihedral_angle_4_deg 12.969 r_dihedral_angle_1_deg 6.374 r_angle_refined_deg 1.287 r_angle_other_deg 1.181 r_chiral_restr 0.05 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 2181 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement Coot model building PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing