3QH1

Structure of Thermolysin in complex with N-benzyloxycarbonyl-L-aspartic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8TLNPDB entry 8TLN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298THERMOLYSIN WAS DISSOLVED IN 30% DMSO, 36mM TRIS/HCl, 1M CALCIUM ACETATE pH 6.3 AT 100MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.503α = 90
b = 92.503β = 90
c = 130.102γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.075NSLSX12C

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
11.551001000.0870.10727.119.4482594825919.3

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 8TLN1.5534.1145590243499.550.115090.113180.15033RANDOM15.863
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]
-0.1-0.05-0.10.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.331
r_dihedral_angle_4_deg14.738
r_dihedral_angle_3_deg11.849
r_scangle_it5.9
r_dihedral_angle_1_deg5.494
r_scbond_it4.28
r_mcangle_it2.649
r_mcbond_it1.838
r_rigid_bond_restr1.742
r_angle_refined_deg1.642
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.331
r_dihedral_angle_4_deg14.738
r_dihedral_angle_3_deg11.849
r_scangle_it5.9
r_dihedral_angle_1_deg5.494
r_scbond_it4.28
r_mcangle_it2.649
r_mcbond_it1.838
r_rigid_bond_restr1.742
r_angle_refined_deg1.642
r_angle_other_deg1.075
r_mcbond_other0.649
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2432
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms24

Software

Software
Software NamePurpose
CBASSdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling