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PanDDA analysis group deposition -- IDOL RING domain in complex with Z1587220559
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9SA2 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 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.7 α = 90 b = 48.02 β = 90.85 c = 70.53 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 2025-02-12 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92203 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 1.44 32.72 98 0.092 0.1 0.038 0.998 11.4 6.5 53065 20.64
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 1.44 1.48 95.3 1.801 2.018 0.893 0.365 4.9 3792
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 9SA2 1.44 20.93 53037 2606 97.7 0.1739 0.1727 0.1978 0.1945 RANDOM 27.94
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] 2.1377 0.6175 1.0307 -3.1684
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.23 t_omega_torsion 3.97 t_angle_deg 1.12 t_bond_d 0.011 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 14.23 t_omega_torsion 3.97 t_angle_deg 1.12 t_bond_d 0.011 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 2197 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 26
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing