4PID

Crystal structure of human adenovirus 2 protease with a weak pyrimidine 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 DROP7.52930.8 M sodium/potassium tartrate, 0.1 M HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.7867.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.783α = 90
b = 112.783β = 90
c = 50.347γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-11-20MSINGLE 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
11.5997.71000.0630.06622.951049317-324.337
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)
11.591.631000.5420.5714.28

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 1NLN1.5948.844931624661000.16610.16480.1892RANDOM18.571
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]
0.010.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.765
r_dihedral_angle_4_deg14.693
r_dihedral_angle_3_deg14.181
r_scangle_it6.645
r_dihedral_angle_1_deg6.232
r_scbond_it4.302
r_mcangle_it2.928
r_angle_refined_deg2.786
r_mcbond_it1.723
r_chiral_restr0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.765
r_dihedral_angle_4_deg14.693
r_dihedral_angle_3_deg14.181
r_scangle_it6.645
r_dihedral_angle_1_deg6.232
r_scbond_it4.302
r_mcangle_it2.928
r_angle_refined_deg2.786
r_mcbond_it1.723
r_chiral_restr0.21
r_bond_refined_d0.034
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1715
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms22

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction