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Structural comparison of cellular retinoic acid binding protein 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 1CBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 PEG mixture
Crystal Properties Matthews coefficient Solvent content 2.77 55.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.89 α = 90 b = 109.98 β = 90 c = 170.34 γ = 90
Symmetry Space Group I 2 2 2
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 2018-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.64 36.05 99.9 0.029 0.029 0.029 0.999 9.8 1.9 43110
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 1.64 1.67 0.791 0.559 0.559 0.48 1.9
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 1CBR 1.64 36.05 43108 2049 99.861 0.193 0.1914 0.1899 0.2184 0.2169 35.424
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] 0.028 0.248 -0.277
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.657 r_dihedral_angle_4_deg 17.956 r_dihedral_angle_3_deg 14.001 r_lrange_it 9.073 r_lrange_other 9.067 r_scangle_it 7.779 r_scangle_other 7.777 r_dihedral_angle_1_deg 6.95 r_scbond_it 5.098 r_scbond_other 5.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.657 r_dihedral_angle_4_deg 17.956 r_dihedral_angle_3_deg 14.001 r_lrange_it 9.073 r_lrange_other 9.067 r_scangle_it 7.779 r_scangle_other 7.777 r_dihedral_angle_1_deg 6.95 r_scbond_it 5.098 r_scbond_other 5.096 r_mcangle_it 4.661 r_mcangle_other 4.66 r_mcbond_it 3.44 r_mcbond_other 3.439 r_angle_refined_deg 1.699 r_angle_other_deg 1.433 r_symmetry_xyhbond_nbd_refined 0.629 r_symmetry_nbd_refined 0.285 r_xyhbond_nbd_refined 0.211 r_nbd_other 0.208 r_nbd_refined 0.198 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.166 r_ncsr_local_group_1 0.115 r_symmetry_nbtor_other 0.095 r_chiral_restr 0.087 r_symmetry_xyhbond_nbd_other 0.082 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 2171 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling Coot model building PHASER phasing XDS data processing XDS data reduction