3QGO

Structure of Thermolysin in complex with L-Phenylalanine methylester


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. Crystals were grown against a well solution containing water, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3347.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.066α = 90
b = 93.066β = 90
c = 128.171γ = 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 X12B1.075NSLSX12B

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
11.454299.50.0920.07154.423.3584965820417.8
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)
11.451.4898.70.8224.622.9

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 8TLN1.4540.35499354993293299.190.112230.112230.110630.142RANDOM13.81
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]
-0.19-0.09-0.190.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.535
r_dihedral_angle_4_deg15.437
r_dihedral_angle_3_deg11.744
r_dihedral_angle_1_deg5.704
r_scangle_it5.436
r_scbond_it3.937
r_mcangle_it2.46
r_angle_refined_deg1.732
r_mcbond_it1.712
r_rigid_bond_restr1.523
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.535
r_dihedral_angle_4_deg15.437
r_dihedral_angle_3_deg11.744
r_dihedral_angle_1_deg5.704
r_scangle_it5.436
r_scbond_it3.937
r_mcangle_it2.46
r_angle_refined_deg1.732
r_mcbond_it1.712
r_rigid_bond_restr1.523
r_angle_other_deg1.037
r_mcbond_other0.609
r_chiral_restr0.139
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms457
Heterogen Atoms94

Software

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