3LIV

crystal structure of HTLV protease complexed with the inhibitor KNI-10683


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B7F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.229317%PEG8000 adn 16% PEG300 0.2M KH2PO4, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8356.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.772α = 90
b = 77.772β = 90
c = 162.972γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.5950940.07825.48.29072-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6958.30.2194.92.1

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 REPLACEMENTTHROUGHOUT2B7F2.5950878226893.840.202450.200630.26219RANDOM22.84
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]
-1.02-0.51-1.021.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.778
r_dihedral_angle_3_deg19.705
r_dihedral_angle_4_deg14.493
r_dihedral_angle_1_deg6.679
r_scangle_it3.937
r_mcangle_it3.851
r_scbond_it2.434
r_mcbond_it2.31
r_angle_refined_deg1.694
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.778
r_dihedral_angle_3_deg19.705
r_dihedral_angle_4_deg14.493
r_dihedral_angle_1_deg6.679
r_scangle_it3.937
r_mcangle_it3.851
r_scbond_it2.434
r_mcbond_it2.31
r_angle_refined_deg1.694
r_chiral_restr0.102
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1766
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms47

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling