4ZIU

Crystal structure of native alpha-2-macroglobulin from Escherichia coli spanning the residues from domain MG7 to the C-terminus.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherdataset of a Se-Met crystal collected at the selenium absorption peak and a native dataset to higher resolution

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9293.1520% [w/v] PEG4,000, 10% isopropanol 100mM Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
3.6666.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.72α = 90
b = 136.19β = 90
c = 172.8γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-02-09MMAD
21x-ray100PIXELDECTRIS PILATUS 6M2012-11-03MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.9763, 0.9788ALBAXALOC
2SYNCHROTRONESRF BEAMLINE ID290.9763, 0.9788ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.74899.40.04824.36.4283502835086
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.7795.30.6542.96.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUTdataset of a Se-Met crystal collected at the selenium absorption peak and a native dataset to higher resolution2.747.982834974799.440.19160.19030.2399RANDOM80.34
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]
-18.477811.27817.1997
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion3.28
t_omega_torsion3.16
t_angle_deg1.16
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion3.28
t_omega_torsion3.16
t_angle_deg1.16
t_bond_d0.01
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 AtomsNumber
Protein Atoms4920
Nucleic Acid Atoms
Solvent Atoms96
Heterogen Atoms32

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
Cootmodel building
BUSTERrefinement