☰ Navigation Tabs
Crystal structure of native alpha-2-macroglobulin from Escherichia coli spanning the residues from domain MG7 to the C-terminus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other dataset of a Se-Met crystal collected at the selenium absorption peak and a native dataset to higher resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293.15 20% [w/v] PEG4,000,
10% isopropanol
100mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 3.66 66.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.72 α = 90 b = 136.19 β = 90 c = 172.8 γ = 90
Symmetry Space Group I 2 2 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 PIXEL DECTRIS PILATUS 6M 2013-02-09 M MAD 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2012-11-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9763, 0.9788 ALBA XALOC 2 SYNCHROTRON ESRF BEAMLINE ID29 0.9763, 0.9788 ESRF ID29
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 48 99.4 0.048 24.3 6.4 28350 28350 86
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 2.77 95.3 0.654 2.9 6.6
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 SIRAS THROUGHOUT dataset of a Se-Met crystal collected at the selenium absorption peak and a native dataset to higher resolution 2.7 47.98 28349 747 99.44 0.1916 0.1903 0.1946 0.2399 0.2426 RANDOM 80.34
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] -18.4778 11.2781 7.1997
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.28 t_omega_torsion 3.16 t_angle_deg 1.16 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.28 t_omega_torsion 3.16 t_angle_deg 1.16 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4920 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 32
Software Software Software Name Purpose XDS data reduction XSCALE data scaling SHELXDE phasing Coot model building BUSTER refinement