☰ Navigation Tabs
De Novo Rhodamine Binder, Rhobin9, binds to Rhodamine 101
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Chai-1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293.15 0.1 M Zinc acetate, 0.1 M MES pH 6, 10% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.886 α = 90 b = 29.876 β = 93.08 c = 68.723 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 EIGER X 16M 2025-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97931 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 2.21 31.3 92.7 0.288 0.336 0.171 0.951 2.5 3.7 13161
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 2.21 2.33 82.4 1.282 1.527 0.814 0.885 3.5
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 2.7 31.299 1.33 7498 748 94.95 0.3108 0.3079 0.309 0.3362 0.34
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 26.104 f_angle_d 0.948 f_chiral_restr 0.048 f_plane_restr 0.016 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 74
Software Software Software Name Purpose PHENIX refinement Aimless data scaling autoPROC data reduction PHENIX phasing