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Crystal structure of the R132K:R111L:T54E mutant of cellular retinoic acid-binding protein II complexed with C15-aldehyde (a retinal analog) at 2.00 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 5.8 277 0.1M sodium acetate, 18% PEG6000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.75 67.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.499 α = 90 b = 87.499 β = 90 c = 210.99 γ = 120
Symmetry Space Group P 61 2 2
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 2007-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97869 APS 21-ID-F
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 1.9 75.8 99.9 0.074 56.1 16.9 38649 1
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) 1.9 1.97 99 0.473 4.2 12
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 (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 2 43.75 31499 1678 99.97 0.19729 0.19539 0.2138 0.23285 0.2456 RANDOM 22.9
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] 1.12 0.56 1.12 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.679 r_dihedral_angle_4_deg 19.711 r_dihedral_angle_3_deg 14.918 r_dihedral_angle_1_deg 5.891 r_mcangle_it 1.918 r_scangle_it 1.895 r_angle_refined_deg 1.449 r_scbond_it 1.301 r_mcbond_it 1.283 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.679 r_dihedral_angle_4_deg 19.711 r_dihedral_angle_3_deg 14.918 r_dihedral_angle_1_deg 5.891 r_mcangle_it 1.918 r_scangle_it 1.895 r_angle_refined_deg 1.449 r_scbond_it 1.301 r_mcbond_it 1.283 r_nbtor_refined 0.325 r_nbd_refined 0.278 r_symmetry_hbond_refined 0.247 r_xyhbond_nbd_refined 0.215 r_symmetry_vdw_refined 0.199 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2305 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling