☰ Navigation Tabs
Redesigned nitrobindin to bind fluorescent ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Rosetta Design
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.04 M Potassium phosphate monobasic
16 % w/v PEG 8000
20 % v/v Glycerol
Crystal Properties Matthews coefficient Solvent content 1.97 37.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.86 α = 90 b = 73.16 β = 95.25 c = 58.98 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 80 PIXEL DECTRIS EIGER2 X 16M 2022-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.78 45.8 90.89 0.997 6.79 3.6 59666 27.24
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 1.78 1.84 0.417
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 1.78 45.8 0.02 27964 1408 90.89 0.18 0.1778 0.1785 0.2218 0.2243 40.23
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 15.1738 f_angle_d 0.5843 f_chiral_restr 0.0493 f_plane_restr 0.0044 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2440 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 63
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing