3RUO

Complex structure of HevB EV93 main protease 3C with Rupintrivir (AG7088)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q3YPDB entry 3Q3Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52930.25 M MgCl2, 0.1 M Tris, 25% PEG 8k, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9336.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.995α = 90
b = 63.911β = 90.43
c = 66.357γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2011-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.872600ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.53010052513-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.55100

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3Q3Y1.5304952349523265899.980.167450.167450.165810.19796RANDOM16.921
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]
-0.240.070.72-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.196
r_dihedral_angle_4_deg18.193
r_dihedral_angle_3_deg11.828
r_dihedral_angle_1_deg5.905
r_scangle_it3.733
r_scbond_it2.325
r_angle_refined_deg1.409
r_mcangle_it1.028
r_mcbond_it0.528
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.196
r_dihedral_angle_4_deg18.193
r_dihedral_angle_3_deg11.828
r_dihedral_angle_1_deg5.905
r_scangle_it3.733
r_scbond_it2.325
r_angle_refined_deg1.409
r_mcangle_it1.028
r_mcbond_it0.528
r_chiral_restr0.088
r_bond_refined_d0.008
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2842
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms89

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling