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Structural comparison of cellular retinoic acid binding proteins I and II in the presence and absence of natural and synthetic ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 PEG based vapor diffusion
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.56 α = 90 b = 78.56 β = 90 c = 78.56 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PILATUS 6M 2019-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9763 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.71 45.398 100 0.077 0.082 0.026 0.999 18.8 18.3 17775
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 1.71 1.74 2.227 2.356 0.76 0.548 18.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5OBG 1.71 45.398 17753 889 99.955 0.181 0.1802 0.2011 0.2121 37.241
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 r_dihedral_angle_2_deg 36.326 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_4_deg 12.3 r_lrange_it 7.715 r_lrange_other 7.712 r_dihedral_angle_1_deg 7.502 r_scangle_it 6.876 r_scangle_other 6.872 r_scbond_it 4.475 r_scbond_other 4.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.326 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_4_deg 12.3 r_lrange_it 7.715 r_lrange_other 7.712 r_dihedral_angle_1_deg 7.502 r_scangle_it 6.876 r_scangle_other 6.872 r_scbond_it 4.475 r_scbond_other 4.473 r_mcangle_other 4.063 r_mcangle_it 4.048 r_mcbond_it 3.231 r_mcbond_other 3.079 r_angle_refined_deg 1.754 r_angle_other_deg 1.421 r_symmetry_nbd_refined 0.338 r_nbd_refined 0.199 r_symmetry_nbd_other 0.182 r_symmetry_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.161 r_nbd_other 0.133 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1091 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data reduction XDS data processing PHASER phasing Coot model building