☰ Navigation Tabs
beta-lactoglobulin in complex with Perfluorodecanoic acid (PFDA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 1.8 M sodium phosphate monobasic monohydrate and potassium phosphate dibasic at pH 8.2
Crystal Properties Matthews coefficient Solvent content 2.46746182 50.1821747
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.023 α = 90 b = 53.023 β = 90 c = 111.157 γ = 120
Symmetry Space Group P 32 2 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 2024-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54184
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 2 28.84 100 1 23.9 14.39 12824
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 2 2.05 100 0.903 4.1 10.95
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold 2 22.495 12781 638 99.844 0.191 0.1886 0.1888 0.2384 0.2384 38.765
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] 0.024 0.012 0.024 -0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.334 r_dihedral_angle_6_deg 13.973 r_dihedral_angle_2_deg 10.393 r_lrange_it 9.835 r_dihedral_angle_1_deg 6.93 r_scangle_it 6.698 r_scbond_it 4.463 r_mcangle_it 3.858 r_mcbond_it 2.613 r_angle_refined_deg 1.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.334 r_dihedral_angle_6_deg 13.973 r_dihedral_angle_2_deg 10.393 r_lrange_it 9.835 r_dihedral_angle_1_deg 6.93 r_scangle_it 6.698 r_scbond_it 4.463 r_mcangle_it 3.858 r_mcbond_it 2.613 r_angle_refined_deg 1.974 r_nbtor_refined 0.314 r_xyhbond_nbd_refined 0.289 r_symmetry_nbd_refined 0.289 r_nbd_refined 0.269 r_symmetry_xyhbond_nbd_refined 0.198 r_chiral_restr 0.134 r_metal_ion_refined 0.024 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1249 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing