3EDI

Crystal structure of tolloid-like protease 1 (TLL-1) protease domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DLE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.527725% PEG 3350, 200mM lithium sulphate, 100mM Bis-Tris-HCl, pH 7.5, vapor diffusion, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4349.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.281α = 90
b = 58.923β = 104.62
c = 47.444γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9999SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.458.996.30.0730.04415.93.54339841793-320.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4474.10.4790.3272.92.662592

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 REPLACEMENTTHROUGHOUT1DLE1.429.9641791209096.390.1550.1540.182RANDOM18.521
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]
-0.14-0.080.11-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.716
r_dihedral_angle_4_deg16.797
r_dihedral_angle_3_deg12.887
r_sphericity_free7.68
r_dihedral_angle_1_deg6.135
r_sphericity_bonded5.158
r_scangle_it5.07
r_scbond_it4.873
r_rigid_bond_restr4.479
r_mcangle_it2.747
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.716
r_dihedral_angle_4_deg16.797
r_dihedral_angle_3_deg12.887
r_sphericity_free7.68
r_dihedral_angle_1_deg6.135
r_sphericity_bonded5.158
r_scangle_it5.07
r_scbond_it4.873
r_rigid_bond_restr4.479
r_mcangle_it2.747
r_mcbond_it1.843
r_angle_refined_deg1.473
r_symmetry_hbond_refined0.591
r_symmetry_vdw_refined0.365
r_nbtor_refined0.312
r_nbd_refined0.288
r_xyhbond_nbd_refined0.256
r_chiral_restr0.103
r_metal_ion_refined0.034
r_bond_refined_d0.016
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1598
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms24

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction