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Crystal structure of de novo designed light-responsive heterodimer 2 (LRD-2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Computational designed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 24% (w/v) PEG 1500, 20% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 3.12 60.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.701 α = 90 b = 63.447 β = 94.88 c = 123.334 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 RIGAKU HyPix-6000HE 2024-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.5
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 30 93.18 0.1628 0.05728 0.976 12.28 12.28 30407
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.258 0.4552 0.154 0.927
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 2.18 29.51 0.02 28400 1455 93.25 0.2598 0.2589 0.259 0.2767 0.2768
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 3.961 f_angle_d 1.167 f_chiral_restr 0.059 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2990 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX phasing CrysalisPro data reduction CrysalisPro data scaling