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Crystal Structure of a Single-chain Trimer of Human Adiponectin Globular Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C28
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 22% PEG3350, 0.1M Bis-Tris, and 25% PEG200, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.88 34.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.31 α = 117.23 b = 49.63 β = 101.68 c = 50.46 γ = 105.31
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 315 mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
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 43.2 91 0.065 10.5 3.2 22892 72800 2 24
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 2.11 72.2 0.323 3 3.1 2655
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 1C28 2 30 21717 1166 90.99 0.2029 0.19992 0.2025 0.25693 0.2526 RANDOM 31.485
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] 2.3 0.57 -0.5 -1.52 -0.16 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.928 r_dihedral_angle_3_deg 15.83 r_dihedral_angle_4_deg 15.282 r_dihedral_angle_1_deg 6.027 r_scangle_it 1.645 r_scbond_it 1.111 r_angle_refined_deg 1.07 r_mcangle_it 0.729 r_mcbond_it 0.407 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.928 r_dihedral_angle_3_deg 15.83 r_dihedral_angle_4_deg 15.282 r_dihedral_angle_1_deg 6.027 r_scangle_it 1.645 r_scbond_it 1.111 r_angle_refined_deg 1.07 r_mcangle_it 0.729 r_mcbond_it 0.407 r_chiral_restr 0.08 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3284 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 30
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling