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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 5OGB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 PEG based
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.55 α = 90 b = 49.92 β = 96.03 c = 67.38 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2018-03-10 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 1.82 49.92 97.6 0.065 0.089 0.061 0.996 10.4 3.5 23023
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 1.82 1.86 0.735 1.003 0.678 0.486 3.7
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 5OGB 1.82 40.064 23016 1125 97.53 0.199 0.1967 0.1982 0.2452 0.2517 29.068
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] -0.042 0.705 -1.062 0.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.454 r_dihedral_angle_3_deg 14.034 r_dihedral_angle_4_deg 14.029 r_dihedral_angle_1_deg 7.953 r_lrange_it 6.655 r_lrange_other 6.633 r_scangle_it 5.265 r_scangle_other 5.264 r_mcangle_other 3.303 r_mcangle_it 3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.454 r_dihedral_angle_3_deg 14.034 r_dihedral_angle_4_deg 14.029 r_dihedral_angle_1_deg 7.953 r_lrange_it 6.655 r_lrange_other 6.633 r_scangle_it 5.265 r_scangle_other 5.264 r_mcangle_other 3.303 r_mcangle_it 3.3 r_scbond_other 3.287 r_scbond_it 3.286 r_mcbond_it 2.296 r_mcbond_other 2.292 r_angle_refined_deg 1.55 r_angle_other_deg 1.281 r_symmetry_xyhbond_nbd_refined 0.308 r_symmetry_nbd_refined 0.199 r_nbd_other 0.191 r_xyhbond_nbd_refined 0.19 r_nbd_refined 0.186 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.163 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.072 r_symmetry_xyhbond_nbd_other 0.015 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2178 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data reduction PHASER phasing Coot model building XDS data processing