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Decameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy- 2-methyl-1,3-dioxane]- 5-yloxycarbonyl}-piperazine
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 sodium acetate, calcium acetate, PEG 8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.861 α = 90 b = 95.054 β = 98.74 c = 164.257 γ = 90
Symmetry Space Group P 1 21 1
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 2003-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115872 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 3 59.8 0.071 0.071 14.4 3.2 45367 45367 -3 -3
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 3 3.11 85.3 0.349 2.2 2.9
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 (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 3 50 43001 42996 2298 95 0.23087 0.22815 0.2118 0.28223 0.2604 RANDOM 11.892
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] 3.74 1.08 -3.66 0.25
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.674 r_dihedral_angle_1_deg 5.495 r_scbond_it 4.351 r_mcangle_it 2.557 r_mcbond_it 1.643 r_angle_refined_deg 1.074 r_symmetry_vdw_refined 0.193 r_nbd_refined 0.182 r_metal_ion_refined 0.155 r_xyhbond_nbd_refined 0.113
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.674 r_dihedral_angle_1_deg 5.495 r_scbond_it 4.351 r_mcangle_it 2.557 r_mcbond_it 1.643 r_angle_refined_deg 1.074 r_symmetry_vdw_refined 0.193 r_nbd_refined 0.182 r_metal_ion_refined 0.155 r_xyhbond_nbd_refined 0.113 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.101 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other 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 16490 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing