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Crystal structure of Q108K:K40L:T51V:T53C:R58W:T29L:Y19W:Q4A mutant of cellular retinol binding protein II complex with all-trans-retinal in the dark
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QYN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 30% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate, pH 4.6, evaporation, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.06 40.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.842 α = 85.95 b = 35.918 β = 86.434 c = 64.062 γ = 65.334
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate 2019-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.000 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.4 30 88.28 0.107 0.06 13 3.1 47394 12.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45 0.291 0.163 4.33
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 4QYN 1.4 29.63 2.07 42052 2068 85.29 0.1757 0.1747 0.1751 0.1964 0.1979 16.83
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 13.26 f_angle_d 0.7936 f_chiral_restr 0.0796 f_bond_d 0.0051 f_plane_restr 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2188 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing