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Crystal Structure of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.55 Angstroms Resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 30% (w/v) PEG 8000, 0.1 M Tris-HCl pH 8.0, and 0.2 M Sodium Acetate, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.475 α = 73.09 b = 37.22 β = 75.74 c = 57.597 γ = 87.22
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 2 1
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 1.55 50 92.3 0.042 23.7 2.2 38968 35956 -3 18.7
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) 1.55 1.61 68.1 68.1 0.157 3.36 2
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 1.55 50 35954 35954 3595 92.45 0.149 0.149 0.144 0.201 0.2137 RANDOM 18.544
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] -0.63 -0.76 0.73 -1.11 -0.46 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.574 r_dihedral_angle_4_deg 19.155 r_dihedral_angle_3_deg 11.864 r_sphericity_free 7.673 r_dihedral_angle_1_deg 6.711 r_scangle_it 4.916 r_scbond_it 3.712 r_sphericity_bonded 3.214 r_mcangle_it 2.515 r_mcbond_it 2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.574 r_dihedral_angle_4_deg 19.155 r_dihedral_angle_3_deg 11.864 r_sphericity_free 7.673 r_dihedral_angle_1_deg 6.711 r_scangle_it 4.916 r_scbond_it 3.712 r_sphericity_bonded 3.214 r_mcangle_it 2.515 r_mcbond_it 2.12 r_rigid_bond_restr 2.081 r_angle_refined_deg 1.742 r_angle_other_deg 0.888 r_mcbond_other 0.688 r_symmetry_vdw_other 0.254 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.199 r_nbd_other 0.197 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.17 r_chiral_restr 0.113 r_nbtor_other 0.086 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 2163 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction