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Crystal Structure of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.35 Angstroms Resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 30% (w/v) PEG 8000 (4000), 0.1 M TRIS-HCl pH 8.0 (8.5), and 0.2 M Sodium Acetate, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.449 α = 72.68 b = 37.056 β = 76.37 c = 56.527 γ = 87.28
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 2005-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.000 APS 14-ID-B
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 1.35 50 88.4 0.042 14.56 2 56961 50380 -3 15.4
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) 1.35 1.4 56.5 56.5 0.261 1.77 1.8
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 1.35 17.24 50364 50364 5082 88.4 0.154 0.154 0.148 0.1503 0.204 0.2043 RANDOM 16.794
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] -1.46 -0.28 0.3 -0.4 -0.2 1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.191 r_dihedral_angle_4_deg 15.157 r_dihedral_angle_3_deg 12.741 r_sphericity_free 7.239 r_dihedral_angle_1_deg 6.818 r_scangle_it 4.846 r_scbond_it 3.391 r_sphericity_bonded 3.354 r_mcangle_it 2.619 r_rigid_bond_restr 1.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.191 r_dihedral_angle_4_deg 15.157 r_dihedral_angle_3_deg 12.741 r_sphericity_free 7.239 r_dihedral_angle_1_deg 6.818 r_scangle_it 4.846 r_scbond_it 3.391 r_sphericity_bonded 3.354 r_mcangle_it 2.619 r_rigid_bond_restr 1.996 r_angle_refined_deg 1.775 r_mcbond_it 1.774 r_angle_other_deg 0.898 r_mcbond_other 0.748 r_symmetry_vdw_other 0.26 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.221 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.196 r_symmetry_hbond_refined 0.183 r_nbtor_refined 0.177 r_metal_ion_refined 0.153 r_chiral_restr 0.118 r_nbtor_other 0.085 r_bond_refined_d 0.018 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 2199 Nucleic Acid Atoms Solvent Atoms 427 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction