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PanDDA analysis group deposition -- IDOL RING domain in complex with Z1685106505
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9SA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 200 mM Sodium acetate, 100 mM Tris, 30% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.15 42.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.588 α = 90 b = 47.937 β = 90.82 c = 70.844 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 EIGER2 XE 9M 2025-02-17 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92205 Diamond I04-1
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 1.71 39.7 99.7 0.324 0.351 0.133 0.987 4.4 6.9 32591 26.32
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 1.71 1.74 95.3 4.776 5.164 1.95 0.456 6.9 1627
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 FOURIER SYNTHESIS THROUGHOUT 9SA2 1.708 29.77 32116 1576 98.3 0.2318 0.2302 0.223 0.2652 0.255 RANDOM 38.3
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] 11.8249 -0.4316 12.6021 -24.427
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.96 t_omega_torsion 3.22 t_angle_deg 1.01 t_bond_d 0.009 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 15.96 t_omega_torsion 3.22 t_angle_deg 1.01 t_bond_d 0.009 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 2152 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 23
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing