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Human NR4A1 ligand-binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YJE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 300 15 % PEG 6000, 0.1 M BISTRIS PH 6.4, 0.4 M SODIUM THIOCYANATE, AND 5 % ETHYLENGLYCOL, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.63 53.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.53 α = 90 b = 96.364 β = 90 c = 144.849 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 100 CCD ADSC QUANTUM 4 2006-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 100 98.9 31070
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 100
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 1yje 2.8 48.17 29394 1566 98.5 0.233 0.23 0.2273 0.292 0.2933 RANDOM 55.78
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] -0.15 0.61 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.58 r_dihedral_angle_3_deg 21.785 r_dihedral_angle_4_deg 21.171 r_dihedral_angle_1_deg 6.837 r_scangle_it 2.795 r_scbond_it 1.695 r_angle_refined_deg 1.635 r_mcangle_it 1.148 r_mcbond_it 0.63 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.58 r_dihedral_angle_3_deg 21.785 r_dihedral_angle_4_deg 21.171 r_dihedral_angle_1_deg 6.837 r_scangle_it 2.795 r_scbond_it 1.695 r_angle_refined_deg 1.635 r_mcangle_it 1.148 r_mcbond_it 0.63 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.313 r_symmetry_hbond_refined 0.253 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.138 r_chiral_restr 0.104 r_bond_refined_d 0.015 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 7137 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling