3QH5

Structure of Thermolysin in complex with N-Carbobenzyloxy-L-aspartic acid and L-Phenylalanine Methyl Ester


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
2.3247.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.686α = 90
b = 92.686β = 90
c = 128.764γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210monochromatic vertical focusing2010-12-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F20.9202CHESSF2

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
11.510099.70.0580.09222.913.45287852719
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)
11.51.53998.10.9070.8992.110.35082

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 8TLN1.527.445281649604265298.940.145760.145760.14360.18707RANDOM15.555
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]
-0.05-0.02-0.050.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.559
r_dihedral_angle_4_deg16.229
r_dihedral_angle_3_deg11.784
r_dihedral_angle_1_deg5.642
r_scangle_it4.841
r_scbond_it3.364
r_mcangle_it2.117
r_angle_refined_deg1.468
r_mcbond_it1.379
r_rigid_bond_restr1.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.559
r_dihedral_angle_4_deg16.229
r_dihedral_angle_3_deg11.784
r_dihedral_angle_1_deg5.642
r_scangle_it4.841
r_scbond_it3.364
r_mcangle_it2.117
r_angle_refined_deg1.468
r_mcbond_it1.379
r_rigid_bond_restr1.248
r_angle_other_deg0.95
r_mcbond_other0.446
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.007
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 Atoms277
Heterogen Atoms84

Software

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