☰ Navigation Tabs
Crystal structure of KRasG12V-Nanobody84
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L9S 4L9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 3350 21%, MES 0.1 M pH 6.0, NaCl 150mM
Crystal Properties Matthews coefficient Solvent content 2.3 46.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.85 α = 90 b = 130.5 β = 116.25 c = 55.6 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 2018-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
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 1.84 42.3 98.6 0.99 10.7 4.7 54015 33.43
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 1.85 1.96 0.66
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4L9S 1.85 42.3 1.38 53978 2698 98.82 0.2023 0.2008 0.2008 0.2303 0.2299 41.19
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 16.5781 f_angle_d 0.7544 f_chiral_restr 0.0603 f_bond_d 0.0058 f_plane_restr 0.0044
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4263 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing