☰ Navigation Tabs
Decameric structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2-carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LGN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 PEG 4000, PEG 400, sodium acetate, calcium acetate, sorbitol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.712 α = 86.53 b = 105.325 β = 78.15 c = 146.007 γ = 76.78
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 2004-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115879 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 60 97.1 0.043 0.043 15.5 2 269382 269382 -3 -3 35.1
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 2.2 2.28 95.6 0.231 3.2 1.9 26464
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1LGN 2.2 100 269370 269370 13598 97.11 0.19005 0.19005 0.18798 0.2137 0.2293 0.2461 RANDOM 17.077
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] -0.99 -0.78 0.35 0.79 1.14 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.242 r_scangle_it 3.901 r_scbond_it 2.629 r_mcangle_it 1.494 r_angle_refined_deg 1.122 r_mcbond_it 0.827 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.095 r_symmetry_hbond_refined 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.242 r_scangle_it 3.901 r_scbond_it 2.629 r_mcangle_it 1.494 r_angle_refined_deg 1.122 r_mcbond_it 0.827 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.179 r_xyhbond_nbd_refined 0.095 r_symmetry_hbond_refined 0.092 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_metal_ion_refined 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32980 Nucleic Acid Atoms Solvent Atoms 2378 Heterogen Atoms 340
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing