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Crystal structure of the apo R132K:L121E mutant of cellular retinoic acid-binding protein II at 1.68 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 9.5 298 0.1 M Bis-tris-propane, pH 9.5, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.699 α = 105.8 b = 37.271 β = 106.44 c = 60.371 γ = 89.97
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 2008-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.99999 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 1.68 55.56 94.5 0.051 20.8 3.8 30624 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 1.68 1.724 90.95 0.251 4 4.2 2025
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2G7B 1.68 35.74 29087 1536 96.61 0.18259 0.18259 0.18001 0.23095 0.2419 RANDOM 30.287
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] 0.23 0.14 1.74 -0.9 -0.11 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.987 r_dihedral_angle_3_deg 12.138 r_dihedral_angle_4_deg 9.373 r_dihedral_angle_1_deg 5.895 r_mcangle_it 2.182 r_scangle_it 2.056 r_mcbond_it 1.4 r_scbond_it 1.341 r_angle_refined_deg 1.333 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.987 r_dihedral_angle_3_deg 12.138 r_dihedral_angle_4_deg 9.373 r_dihedral_angle_1_deg 5.895 r_mcangle_it 2.182 r_scangle_it 2.056 r_mcbond_it 1.4 r_scbond_it 1.341 r_angle_refined_deg 1.333 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.244 r_symmetry_hbond_refined 0.243 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2180 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling