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The crystal structure of the orphan nuclear receptor PNR ligand binding domain fused with MBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P0U pdb id 3P0U (for PNR), pdb id 1OMP (for MBP) experimental model PDB 1OMP pdb id 3P0U (for PNR), pdb id 1OMP (for MBP)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 298 PEG6000, pH 5.6, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.79 55.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.435 α = 90 b = 184.936 β = 90 c = 85.97 γ = 90
Symmetry Space Group P 21 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 100 CCD MARMOSAIC 300 mm CCD 2011-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0 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 2.7 30 83.8 0.085 20.5 38683 35685 2 2
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 2.7 2.8 67.8 0.0655 2 4.5
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 id 3P0U (for PNR), pdb id 1OMP (for MBP) 2.7 30 35657 2958 96.5 0.28712 0.28544 0.278 0.30744 0.2959 RANDOM 51.63
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] -0.59 -0.95 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.484 r_dihedral_angle_4_deg 17.523 r_dihedral_angle_3_deg 17.114 r_sphericity_free 12.158 r_sphericity_bonded 8.254 r_scangle_it 4.039 r_dihedral_angle_1_deg 3.45 r_rigid_bond_restr 3.397 r_scbond_it 2.793 r_mcangle_it 2.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.484 r_dihedral_angle_4_deg 17.523 r_dihedral_angle_3_deg 17.114 r_sphericity_free 12.158 r_sphericity_bonded 8.254 r_scangle_it 4.039 r_dihedral_angle_1_deg 3.45 r_rigid_bond_restr 3.397 r_scbond_it 2.793 r_mcangle_it 2.451 r_mcbond_it 1.325 r_angle_refined_deg 1.145 r_angle_other_deg 0.852 r_mcbond_other 0.503 r_chiral_restr 0.061 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6172 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection DENZO data reduction