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Crystal Structure of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinoic Acid at 1.48 Angstroms Resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 30% (w/v) PEG 4000, 0.1 M sodium citrate/citric acid pH 5.4, and 0.2 ammonium acetate (crystallization performed in dark room and under red light), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.287 α = 90 b = 46.464 β = 90 c = 77.261 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 2005-07-23 M SINGLE WAVELENGTH 2 1 x-ray M
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 1,2 1.48 39.81 95.5 0.044 28.19 27332 26090 17.1
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) 1.48 1.53 96.4 96.4 0.139 5.08
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Rigid Body Refinement THROUGHOUT 1.48 39.81 23523 23523 2622 95.13 0.131 0.131 0.126 0.174 0.1951 RANDOM 15.735
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] 0.45 0.37 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.653 r_dihedral_angle_3_deg 11.911 r_dihedral_angle_4_deg 9.076 r_sphericity_free 9.057 r_dihedral_angle_1_deg 6.374 r_scangle_it 5.001 r_sphericity_bonded 4.394 r_scbond_it 3.862 r_mcangle_it 2.875 r_mcbond_it 2.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.653 r_dihedral_angle_3_deg 11.911 r_dihedral_angle_4_deg 9.076 r_sphericity_free 9.057 r_dihedral_angle_1_deg 6.374 r_scangle_it 5.001 r_sphericity_bonded 4.394 r_scbond_it 3.862 r_mcangle_it 2.875 r_mcbond_it 2.355 r_rigid_bond_restr 1.932 r_angle_refined_deg 1.815 r_angle_other_deg 1.063 r_mcbond_other 0.954 r_symmetry_vdw_other 0.255 r_symmetry_vdw_refined 0.25 r_nbd_refined 0.216 r_nbd_other 0.203 r_xyhbond_nbd_refined 0.192 r_symmetry_hbond_refined 0.186 r_nbtor_refined 0.178 r_chiral_restr 0.131 r_nbtor_other 0.083 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1101 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction