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Crystal structure of the Pyrococcus abyssi RPA trimerization core bound to poly-dT20 ssDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Working model of the full apo-RPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 10% w/v PEG 8K
0.1M imidazole pH 8
0.2 M calcium acetate
Crystal Properties Matthews coefficient Solvent content 2.4 48.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.234 α = 90 b = 75.234 β = 90 c = 215.487 γ = 120
Symmetry Space Group P 32 2 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 EIGER X 16M KB Mirrors 2021-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.2 48.26 80.7 0.067 0.068 0.013 1 27.1 27.2 10041 163.2
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 3.2 3.28 21.2 4.189 4.27 0.816 0.454 1 26.8
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 Working model of the full apo-RPA 3.2 48.26 10041 494 81.5 0.2655 0.2641 0.2689 0.2933 0.2965 RANDOM 173.43
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] 1.688 1.688 -3.3761
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.91 t_omega_torsion 2.41 t_angle_deg 0.85 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_utility_distance t_utility_angle
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.91 t_omega_torsion 2.41 t_angle_deg 0.85 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_utility_distance t_utility_angle t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3771 Nucleic Acid Atoms 280 Solvent Atoms Heterogen Atoms 6
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling MOLREP phasing MxCuBE data collection Coot model building