5JQB

Crystal structure of Ebola glycoprotein in complex with ibuprofen


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2939% (w/v) PEG 6000 and 0.1 M Sodium citrate tribasic dihydrate
Crystal Properties
Matthews coefficientSolvent content
3.4964.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.76α = 90
b = 113.76β = 90
c = 306.15γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9700DiamondI02

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
12.6882.8499.90.12914.79.821842
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.682.751001.58.3

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 REPLACEMENTTHROUGHOUT5JQ32.6882.8420734110799.90.2010.1990.234RANDOM73.22
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]
0.730.370.73-2.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.628
r_dihedral_angle_4_deg16.894
r_dihedral_angle_3_deg13.758
r_dihedral_angle_1_deg6.468
r_long_range_B_refined5.972
r_long_range_B_other5.971
r_scangle_other3.014
r_mcangle_it2.779
r_mcangle_other2.778
r_scbond_it1.709
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.628
r_dihedral_angle_4_deg16.894
r_dihedral_angle_3_deg13.758
r_dihedral_angle_1_deg6.468
r_long_range_B_refined5.972
r_long_range_B_other5.971
r_scangle_other3.014
r_mcangle_it2.779
r_mcangle_other2.778
r_scbond_it1.709
r_scbond_other1.709
r_mcbond_it1.522
r_mcbond_other1.522
r_angle_refined_deg1.241
r_angle_other_deg0.871
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.004
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 Atoms3025
Nucleic Acid Atoms
Solvent Atoms73
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing