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Crystal Structure of the R132K:Y134F:R111L:T54V:L121E Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-trans-Retinoic Acid at 1.57 Angstroms Resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1 M MES, 30% (W/V) PEG 5000, 0.2 M AMMONIUM SULFATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.787 α = 90 b = 44.86 β = 90 c = 77.865 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 2004-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 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 1.6 50 99.8 0.05 27.28 21826 -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) 1.6 1.66 100 0.157
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 1.6 39.47 19203 2110 97.7 0.125 0.12 0.1356 0.167 0.1743 RANDOM 14.29
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] 0.56 0.13 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.979 r_dihedral_angle_3_deg 12.332 r_dihedral_angle_4_deg 9.868 r_sphericity_free 9.116 r_dihedral_angle_1_deg 6.231 r_scangle_it 5.127 r_scbond_it 3.909 r_sphericity_bonded 3.686 r_mcangle_it 2.57 r_rigid_bond_restr 2.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.979 r_dihedral_angle_3_deg 12.332 r_dihedral_angle_4_deg 9.868 r_sphericity_free 9.116 r_dihedral_angle_1_deg 6.231 r_scangle_it 5.127 r_scbond_it 3.909 r_sphericity_bonded 3.686 r_mcangle_it 2.57 r_rigid_bond_restr 2.305 r_mcbond_it 2.247 r_angle_refined_deg 1.881 r_angle_other_deg 0.965 r_mcbond_other 0.811 r_symmetry_vdw_other 0.314 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.212 r_nbd_other 0.201 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.125 r_nbtor_other 0.086 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1146 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing