4PIE

Crystal structure of human adenovirus 2 protease a substrate based nitrile inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NLNPDB entry 1NLN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62931mM peptide-nitrile inhibitor was added to the protein and incubated for 30 minutes. 0.8M lithium sulphate, 0.1 M sodium acetate, pH 4.6
Crystal Properties
Matthews coefficientSolvent content
1.8633.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.312α = 90
b = 44.437β = 90
c = 98.921γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.9444.499.90.0540.05919.486.414072-334.286
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.941.9999.70.4070.4424.57

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 REPLACEMENTTHROUGHOUTPDB entry 1NLN1.9440.531407270499.950.20960.20690.2603RANDOM31.634
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]
-2.495.01-2.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.728
r_dihedral_angle_3_deg17.297
r_dihedral_angle_4_deg13.089
r_dihedral_angle_1_deg7.102
r_scangle_it4.829
r_scbond_it3.272
r_angle_refined_deg2.049
r_mcangle_it1.903
r_mcbond_it1.113
r_chiral_restr0.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.728
r_dihedral_angle_3_deg17.297
r_dihedral_angle_4_deg13.089
r_dihedral_angle_1_deg7.102
r_scangle_it4.829
r_scbond_it3.272
r_angle_refined_deg2.049
r_mcangle_it1.903
r_mcbond_it1.113
r_chiral_restr0.138
r_bond_refined_d0.024
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1685
Nucleic Acid Atoms
Solvent Atoms33
Heterogen Atoms49

Software

Software
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling