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LIGAND-BINDING DOMAIN OF THE HUMAN RETINOIC ACID RECEPTOR GAMMA BOUND TO 9-CIS RETINOIC ACID
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2LBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.36 33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.666 α = 90 b = 60.666 β = 90 c = 155.134 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 IMAGE PLATE MARRESEARCH 1996-05-18 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LURE BEAMLINE DW32 LURE DW32
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.4 15 98.45 0.074 25.43 4.45 11390
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 97.8 0.3 7.29 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT 2LBD 2.4 5 3 9576 1 84 0.172 0.172 0.267 RANDOM (FREERFLAG, CCP4) 36.2
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 21 x_angle_deg 1.504 x_improper_angle_d 1.48 x_bond_d 0.011 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 21 x_angle_deg 1.504 x_improper_angle_d 1.48 x_bond_d 0.011 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 x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1862 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 22
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement MARXDS data reduction MARSCALE data scaling X-PLOR phasing