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Ruvbl1-Ruvbl2 with truncated domain II in complex with phosphorylated Cordycepin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XSZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.1 M HEPES-Na pH 7.5-7.6, 0.2 M MgCl2, 20-21 % PEG400
Crystal Properties Matthews coefficient Solvent content 2.55 51.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.304 α = 90 b = 186.424 β = 91.04 c = 235.176 γ = 90
Symmetry Space Group C 1 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 2019-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
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 2.502 235.137 89.9 0.107 0.12 0.054 0.996 9.1 4.6 90883 62.45
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 2.502 2.81 1.033 1.138 0.474 0.159
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 2XSZ 2.502 49.72 90867 4436 55.7 0.23 0.228 0.2402 0.269 0.2416 RANDOM 70.63
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] -0.9939 -1.9771 9.0545 -8.0606
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.59 t_omega_torsion 1.98 t_angle_deg 1.07 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.59 t_omega_torsion 1.98 t_angle_deg 1.07 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26860 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 314
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing