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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 3.93 68.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.545 α = 90 b = 127.545 β = 90 c = 52.161 γ = 120
Symmetry Space Group P 31 2 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 PILATUS 6M 2020-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
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 2.41 110.46 99.9 0.107 0.392 0.123 0.994 7.1 19.2 19102
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 2.41 2.5 6.347 6.751 2.287 0.398 16.8
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 2.41 110.457 19078 848 99.806 0.207 0.2047 0.2025 0.25 0.2478 53.96
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] 1.143 0.572 1.143 -3.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.452 r_dihedral_angle_3_deg 17.666 r_dihedral_angle_4_deg 16.601 r_lrange_other 11.723 r_lrange_it 11.718 r_scangle_other 8.258 r_scangle_it 8.255 r_dihedral_angle_1_deg 8.06 r_mcangle_other 7.338 r_mcangle_it 7.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.452 r_dihedral_angle_3_deg 17.666 r_dihedral_angle_4_deg 16.601 r_lrange_other 11.723 r_lrange_it 11.718 r_scangle_other 8.258 r_scangle_it 8.255 r_dihedral_angle_1_deg 8.06 r_mcangle_other 7.338 r_mcangle_it 7.332 r_scbond_other 5.159 r_scbond_it 5.158 r_mcbond_it 4.764 r_mcbond_other 4.747 r_angle_refined_deg 1.559 r_angle_other_deg 1.28 r_symmetry_nbd_refined 0.378 r_nbd_other 0.209 r_nbd_refined 0.195 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.164 r_ncsr_local_group_1 0.154 r_symmetry_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2141 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data processing XDS data reduction PHASER phasing Coot model building Aimless data scaling