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Cellular Retinoic Acid Binding Protein II with Bound Inhibitor 4-[6-({4-[(fluorosulfonyl)oxy]phenyl}ethynyl)-4,4-dimethyl-3,4-dihydroquinolin-1(2H)-yl]-4-oxobutanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HKR PDB entry 6HKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M Sodium Acetate, 18% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.21 44.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.604 α = 90 b = 69.655 β = 90 c = 120.845 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2021-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 50 99.7 0.127 0.139 0.055 19.5 6.4 21965
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 100 0.553 0.602 0.236 0.877 3.57 6.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 6HKR 2 35.057 21586 1083 99.686 0.178 0.1754 0.1853 0.2333 0.2426 Random 24.819
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] 0.02 -0.006 -0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.374 r_dihedral_angle_4_deg 18.851 r_dihedral_angle_3_deg 13.272 r_dihedral_angle_1_deg 7.847 r_lrange_it 6.488 r_lrange_other 6.379 r_scangle_it 5.005 r_scangle_other 4.986 r_scbond_it 3.223 r_scbond_other 3.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.374 r_dihedral_angle_4_deg 18.851 r_dihedral_angle_3_deg 13.272 r_dihedral_angle_1_deg 7.847 r_lrange_it 6.488 r_lrange_other 6.379 r_scangle_it 5.005 r_scangle_other 4.986 r_scbond_it 3.223 r_scbond_other 3.194 r_mcangle_it 2.973 r_mcangle_other 2.973 r_mcbond_it 2.016 r_mcbond_other 2.015 r_angle_refined_deg 1.668 r_angle_other_deg 1.348 r_xyhbond_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.193 r_nbd_refined 0.189 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.167 r_nbd_other 0.144 r_symmetry_nbd_refined 0.123 r_symmetry_xyhbond_nbd_other 0.085 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2214 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing