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Complex of TTR and RBP4 and Oleic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JYD PDB ENTRY 1JYD
Crystallization Crystal Properties Matthews coefficient Solvent content 6.39 80.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.662 α = 90 b = 138.662 β = 90 c = 122.789 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD ADSC CCD 2007-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 2.85 50 99.5 0.06 21.97 7.5 54072
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 2.85 2.99 99.5 0.67 2.95 7.6
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 ENTRY 1JYD 2.85 92.06 51275 2758 99.5 0.2279 0.22655 0.2258 0.25319 0.2526 RANDOM 83.135
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] 2.5 2.5 -5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.664 r_dihedral_angle_3_deg 18.797 r_dihedral_angle_4_deg 18.095 r_dihedral_angle_1_deg 6.39 r_scangle_it 3.256 r_scbond_it 2.021 r_mcangle_it 1.615 r_angle_refined_deg 1.562 r_mcbond_it 0.977 r_symmetry_vdw_refined 0.347
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.664 r_dihedral_angle_3_deg 18.797 r_dihedral_angle_4_deg 18.095 r_dihedral_angle_1_deg 6.39 r_scangle_it 3.256 r_scbond_it 2.021 r_mcangle_it 1.615 r_angle_refined_deg 1.562 r_mcbond_it 0.977 r_symmetry_vdw_refined 0.347 r_nbtor_refined 0.315 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.208 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.1 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6455 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing