4M1U

The crystal structure of Stx2 and a disaccharide ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R4Ppdb entry 1R4P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72973.8 M sodium formate, 50 mM Tris pH 7.0, 2% ethylene glycol, and 1 mM PPS (3-(1-pyridino)-1-propanesulfonate) , VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.5752.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.25α = 90
b = 146.25β = 90
c = 60.31γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2012-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-10.97949CLSI08B1-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.565092.80.0828.8206175104677-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.561.6589.90.9781.42.929975

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1R4P1.56409985399444522999.590.17140.170310.19193RANDOM25.06
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]
-0.17-0.09-0.170.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.566
r_dihedral_angle_4_deg15.039
r_dihedral_angle_3_deg11.644
r_dihedral_angle_1_deg5.336
r_scangle_it1.512
r_angle_refined_deg0.989
r_scbond_it0.943
r_mcangle_it0.619
r_mcbond_it0.32
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.566
r_dihedral_angle_4_deg15.039
r_dihedral_angle_3_deg11.644
r_dihedral_angle_1_deg5.336
r_scangle_it1.512
r_angle_refined_deg0.989
r_scbond_it0.943
r_mcangle_it0.619
r_mcbond_it0.32
r_chiral_restr0.069
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4961
Nucleic Acid Atoms
Solvent Atoms732
Heterogen Atoms93

Software

Software
Software NamePurpose
MxDCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling