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TMEM55B tandem RING-like domains in complex with RILPL1 C-terminal peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8OQH non-complexed TMEM55B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289.15 0.05M KSCN
0.1M Tris pH 8.5
18% PEG5000/MME
Crystal Properties Matthews coefficient Solvent content 1.91 35.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.514 α = 90 b = 48.442 β = 90 c = 79.992 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 EIGER X 16M Horizontal pre-focus bimorph mirror & KB bimorph mirrors 2023-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.9794 NSLS-II 17-ID-2
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 1.55 79.99 99.8 0.15 0.163 0.063 0.998 8.9 6.6 24054 15.08
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 1.55 1.58 99.6 2.242 2.426 0.917 0.536 6.7
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 FREE R-VALUE 1.55 41.44 0.18 24054 2255 99.4 0.2067 0.2047 0.2047 0.2462 0.2462 25.11
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 5.7453 f_angle_d 1.0137 f_chiral_restr 0.062 f_plane_restr 0.0121 f_bond_d 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1266 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing