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Crystal structure of retinol-binding protein 4 in complex with tinlarebant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KT7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 1 M ammonium sulfate, 0.1 M HEPES-NaOH, pH 7
Crystal Properties Matthews coefficient Solvent content 2.98 58.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.158 α = 90 b = 148.158 β = 90 c = 118.448 γ = 120
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 2026-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979458 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.1 50 99.6 0.103 0.998 11.1 5.3 85992 47.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.22 99.7 1.47 0.508 1.17 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 48.5 81400 4090 99.04 0.1977 0.19661 0.2064 0.21852 0.2246 RANDOM 44.97
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] -0.42 -0.21 -0.42 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.559 r_dihedral_angle_1_deg 7.84 r_long_range_B_refined 6.037 r_long_range_B_other 5.996 r_dihedral_angle_2_deg 5.066 r_scangle_other 4.147 r_mcangle_it 2.631 r_mcangle_other 2.631 r_scbond_it 2.541 r_scbond_other 2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.559 r_dihedral_angle_1_deg 7.84 r_long_range_B_refined 6.037 r_long_range_B_other 5.996 r_dihedral_angle_2_deg 5.066 r_scangle_other 4.147 r_mcangle_it 2.631 r_mcangle_other 2.631 r_scbond_it 2.541 r_scbond_other 2.52 r_mcbond_it 1.629 r_mcbond_other 1.628 r_angle_refined_deg 0.874 r_angle_other_deg 0.318 r_chiral_restr 0.046 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8487 Nucleic Acid Atoms Solvent Atoms 753 Heterogen Atoms 289
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing