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Crystal structure of the R132K:R111L:A32E mutant of cellular retinoic acid-binding protein II at 1.56 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G7B PDB entry 2G7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1M Tris, 0.2M NaOAc, 26% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.692 α = 102.55 b = 37.071 β = 106.37 c = 58.549 γ = 92.87
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2007-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0000 APS 21-ID-D
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 1.56 54.6 92.3 0.064 37.2 3.5 35378 1 27.9
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 1.56 1.63 70.7 0.221 5.7 2.8 2740
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2G7B 1.56 25.91 33597 1771 92.31 0.15647 0.15647 0.1542 0.1563 0.19841 0.2017 RANDOM 26.369
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] -1.25 -0.35 -0.43 -1.22 -0.25 2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_3_deg 12.508 r_dihedral_angle_4_deg 11.69 r_dihedral_angle_1_deg 5.607 r_sphericity_free 5.189 r_sphericity_bonded 4.231 r_mcangle_it 3.082 r_rigid_bond_restr 3.06 r_scangle_it 2.821 r_mcbond_it 2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.156 r_dihedral_angle_3_deg 12.508 r_dihedral_angle_4_deg 11.69 r_dihedral_angle_1_deg 5.607 r_sphericity_free 5.189 r_sphericity_bonded 4.231 r_mcangle_it 3.082 r_rigid_bond_restr 3.06 r_scangle_it 2.821 r_mcbond_it 2.57 r_scbond_it 2.224 r_angle_refined_deg 1.525 r_nbtor_refined 0.324 r_symmetry_vdw_refined 0.26 r_nbd_refined 0.251 r_xyhbond_nbd_refined 0.208 r_symmetry_hbond_refined 0.198 r_chiral_restr 0.102 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2083 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 3
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling