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Human XRN1 with Adenosine-3',5'-Bisphosphate (pAp) Bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y35 Residues 1-650
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 293 0.2 M Potassium fluoride, pH 7.3, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.91 α = 90 b = 63.97 β = 90 c = 363.15 γ = 90
Symmetry Space Group P 21 21 21
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 2021-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 48.051 99.98 0.163 10.9 13.1 84285
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.154 100 1.2 2.1 13.5
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 48.051 84285 4332 99.983 0.189 0.1866 0.1866 0.2274 0.2275 44.99
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] -0.002 -0.013 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.366 r_dihedral_angle_6_deg 13.574 r_lrange_it 10.637 r_scangle_it 8.236 r_dihedral_angle_1_deg 6.547 r_dihedral_angle_2_deg 6.197 r_mcangle_it 5.704 r_scbond_it 5.545 r_mcbond_it 4.04 r_angle_refined_deg 1.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.366 r_dihedral_angle_6_deg 13.574 r_lrange_it 10.637 r_scangle_it 8.236 r_dihedral_angle_1_deg 6.547 r_dihedral_angle_2_deg 6.197 r_mcangle_it 5.704 r_scbond_it 5.545 r_mcbond_it 4.04 r_angle_refined_deg 1.799 r_nbtor_refined 0.316 r_symmetry_nbd_refined 0.228 r_nbd_refined 0.223 r_symmetry_xyhbond_nbd_refined 0.207 r_xyhbond_nbd_refined 0.172 r_chiral_restr 0.127 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9252 Nucleic Acid Atoms Solvent Atoms 723 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing Coot model building Aimless data scaling