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PANK3 complex structure with compound PZ-5588
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 PEG 4000, ammonium acetate, citrate
Crystal Properties Matthews coefficient Solvent content 2.28 46.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.431 α = 90 b = 98.431 β = 90 c = 68.795 γ = 120
Symmetry Space Group P 31 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 9M 2024-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9202 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.092 32.219 100 0.113 0.999 13.4 12.9 23058 44.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.092 2.128 100 0.404 1.2 11.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.092 32.219 1.34 23054 1238 99.98 0.1965 0.1943 0.1969 0.2372 0.2289 57.34
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.958 f_angle_d 0.5086 f_chiral_restr 0.0391 f_plane_restr 0.0027 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2707 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement XDS data reduction autoPROC data processing Aimless data scaling PHASER phasing