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Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms Resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 30% (w/v) PEG 8000 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.49 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.493 α = 90 b = 46.325 β = 90 c = 73.597 γ = 90
Symmetry Space Group P 21 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 77 CCD MARRESEARCH 2004-11-27 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 1.000 APS 32-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.69 50 99.6 0.076 17.03 18002 17931 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.69 1.75 99.9 99.9 0.741
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Rigid Body Refinement THROUGHOUT 1.69 39.19 17868 17868 1815 99.4 0.161 0.161 0.155 0.1665 0.214 0.2228 RANDOM 21.178
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] 0.04 0.23 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.157 r_dihedral_angle_3_deg 13.498 r_dihedral_angle_4_deg 12.563 r_sphericity_free 8.352 r_dihedral_angle_1_deg 6.883 r_scangle_it 5.524 r_scbond_it 3.651 r_sphericity_bonded 3.307 r_mcangle_it 2.773 r_rigid_bond_restr 2.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.157 r_dihedral_angle_3_deg 13.498 r_dihedral_angle_4_deg 12.563 r_sphericity_free 8.352 r_dihedral_angle_1_deg 6.883 r_scangle_it 5.524 r_scbond_it 3.651 r_sphericity_bonded 3.307 r_mcangle_it 2.773 r_rigid_bond_restr 2.123 r_angle_refined_deg 1.819 r_mcbond_it 1.801 r_angle_other_deg 0.883 r_mcbond_other 0.731 r_metal_ion_refined 0.304 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.222 r_symmetry_vdw_other 0.215 r_xyhbond_nbd_refined 0.21 r_nbd_other 0.202 r_xyhbond_nbd_other 0.195 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.16 r_chiral_restr 0.117 r_nbtor_other 0.088 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1103 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 51
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction