5JQ3

Crystal structure of Ebola glycoprotein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.22939% (w/v) PEG 6000 and 0.1 M Sodium citrate tribasic dihydrate
Crystal Properties
Matthews coefficientSolvent content
4.4372.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.258α = 90
b = 114.258β = 90
c = 307.377γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I031.07193DiamondI03

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
12.2394.191000.20417.457.838090
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.232.291001.315.4

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 REPLACEMENTTHROUGHOUT3CSY2.2394.1936035186599.50.2230.2220.246RANDOM72.48
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]
0.270.130.27-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.769
r_dihedral_angle_4_deg14.657
r_dihedral_angle_3_deg13.099
r_long_range_B_refined6.465
r_long_range_B_other6.465
r_dihedral_angle_1_deg6.028
r_scangle_other2.738
r_mcangle_it2.327
r_mcangle_other2.326
r_scbond_it1.585
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.769
r_dihedral_angle_4_deg14.657
r_dihedral_angle_3_deg13.099
r_long_range_B_refined6.465
r_long_range_B_other6.465
r_dihedral_angle_1_deg6.028
r_scangle_other2.738
r_mcangle_it2.327
r_mcangle_other2.326
r_scbond_it1.585
r_scbond_other1.585
r_mcbond_it1.257
r_mcbond_other1.257
r_angle_refined_deg1.244
r_angle_other_deg0.852
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms3068
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms143

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing