7JPH

Crystal structure of EBOV glycoprotein with modified HR1c and HR2 stalk at 3.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JQ3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52930.1 M Sodium citrate, 10% PEG w/v 6000
Crystal Properties
Matthews coefficientSolvent content
2.3447.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.061α = 90
b = 114.061β = 90
c = 136.216γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
13.19549.43999.90.7768.48.917343
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.3199.80.3130.45

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5JQ33.19549.4391708283797.650.2790.27660.321693.62
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]
-1.131-0.565-1.1313.668
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.871
r_dihedral_angle_3_deg18.699
r_dihedral_angle_4_deg17.346
r_lrange_it16.706
r_lrange_other16.704
r_scangle_it12.702
r_scangle_other12.7
r_mcangle_it12.408
r_mcangle_other12.407
r_dihedral_angle_1_deg8.753
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.871
r_dihedral_angle_3_deg18.699
r_dihedral_angle_4_deg17.346
r_lrange_it16.706
r_lrange_other16.704
r_scangle_it12.702
r_scangle_other12.7
r_mcangle_it12.408
r_mcangle_other12.407
r_dihedral_angle_1_deg8.753
r_scbond_it7.849
r_scbond_other7.849
r_mcbond_it7.777
r_mcbond_other7.766
r_angle_refined_deg1.799
r_angle_other_deg1.589
r_symmetry_nbd_other0.217
r_nbd_refined0.216
r_nbd_other0.203
r_symmetry_nbd_refined0.196
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.139
r_symmetry_xyhbond_nbd_refined0.133
r_ext_dist_refined_d0.124
r_symmetry_nbtor_other0.094
r_chiral_restr0.087
r_symmetry_xyhbond_nbd_other0.058
r_bond_refined_d0.013
r_bond_other_d0.013
r_gen_planes_refined0.009
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3165
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing