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Crystal structure of the R132K:Y134F:R111L:L121D:T54V mutant of cellular retinoic acid-binding protein II at 1.51 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 7.5 298 0.1M Tris, 0.2M NaOAc, 24% PEG4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.21 44.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.601 α = 73.64 b = 37.189 β = 76.67 c = 57.056 γ = 87.7
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 300 mm CCD 2007-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97850 APS 21-ID-G
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 1.51 53.5 93.3 0.041 46.2 4.2 39062 1 29.6
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 1.51 1.56 70.5 0.232 4.5 3.4 2938
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 1.51 33.66 37100 1961 94.25 0.17579 0.17579 0.17385 0.1755 0.21028 0.213 RANDOM 29.467
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] -0.65 -0.57 0.36 -2.68 0.57 2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.549 r_dihedral_angle_4_deg 16.387 r_dihedral_angle_3_deg 13.856 r_sphericity_free 5.885 r_dihedral_angle_1_deg 5.74 r_sphericity_bonded 5.069 r_scangle_it 3.006 r_mcangle_it 2.913 r_scbond_it 2.334 r_rigid_bond_restr 2.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.549 r_dihedral_angle_4_deg 16.387 r_dihedral_angle_3_deg 13.856 r_sphericity_free 5.885 r_dihedral_angle_1_deg 5.74 r_sphericity_bonded 5.069 r_scangle_it 3.006 r_mcangle_it 2.913 r_scbond_it 2.334 r_rigid_bond_restr 2.316 r_mcbond_it 2.141 r_angle_refined_deg 1.425 r_nbtor_refined 0.323 r_nbd_refined 0.232 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.198 r_chiral_restr 0.093 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 2170 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 15
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling