4WY7

Crystal structure of recombinant 4E10 expressed in Escherichia coli with epitope bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FX7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293.15200 mM sodium acetate 30% PEG 8,000 100 mM sodium cacodylate Protein was prepared in PBS
Crystal Properties
Matthews coefficientSolvent content
2.7755.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.3α = 90
b = 44.58β = 113.8
c = 85.4γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

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
12.144.794.20.102145.530114
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)
12.12.2176.60.374.35.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2FX72.144.728584153093.890.163970.161690.2072RANDOM31.78
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]
-0.660.5-1.130.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.362
r_dihedral_angle_4_deg19.933
r_dihedral_angle_3_deg12.811
r_dihedral_angle_1_deg8.044
r_long_range_B_refined5.948
r_long_range_B_other5.847
r_scangle_other3.949
r_mcangle_it2.959
r_mcangle_other2.959
r_scbond_it2.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.362
r_dihedral_angle_4_deg19.933
r_dihedral_angle_3_deg12.811
r_dihedral_angle_1_deg8.044
r_long_range_B_refined5.948
r_long_range_B_other5.847
r_scangle_other3.949
r_mcangle_it2.959
r_mcangle_other2.959
r_scbond_it2.54
r_scbond_other2.54
r_mcbond_it1.96
r_mcbond_other1.959
r_angle_refined_deg1.526
r_angle_other_deg0.764
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3406
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building