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CELLULAR RETINOIC ACID BINDING PROTEIN II IN COMPLEX WITH A SYNTHETIC RETINOIC ACID (RO-12 7310)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CBS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 20% MONOMETHYL PEG 5000
0.2 M TRIS-HCL
0.2 M LICL
, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.47 50.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.03 α = 90 b = 48.32 β = 90 c = 83.82 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 298 IMAGE PLATE RIGAKU M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1
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 2 45 91.9 0.029 35.1 3.2 10051 13.9
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 2 2.03 93.3 0.11 12.2 3
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1CBS 2 10 10016 820 92.4 0.2 0.2003 0.244 0.2426 RANDOM 24.2
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] -3.45 0.53 2.92
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25.6 x_scangle_it 2.82 x_scbond_it 1.87 x_mcangle_it 1.53 x_angle_deg 1.5 x_mcbond_it 0.94 x_improper_angle_d 0.69 x_bond_d 0.006 x_bond_d_na x_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 25.6 x_scangle_it 2.82 x_scbond_it 1.87 x_mcangle_it 1.53 x_angle_deg 1.5 x_mcbond_it 0.94 x_improper_angle_d 0.69 x_bond_d 0.006 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1091 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 22
Software Software Software Name Purpose AMoRE phasing CNS refinement DENZO data reduction SCALEPACK data scaling