1L3F

Thermolysin in the Absence of Substrate has an Open Conformation


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6298MES, dimethylsulfoxide, NaCl, Zn Acetate, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.665

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.052α = 90
b = 97.052β = 90
c = 106.583γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2.9778SSRLBL9-2

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
12.32596.70.1030.0964.49.12246864
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)
2.32.3679.20.420.541.43.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB MODEL 8TLN2.32522468113896.70.2020.302RANDOM72.1
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]
-1.99-1.993.98
RMS Deviations
KeyRefinement Restraint Deviation
o_dihedral_angle_d3.5
o_angle_deg3.2
o_improper_angle_d0.024
o_bond_d0.016
o_bond_d_na
o_bond_d_prot
o_angle_d
o_angle_d_na
o_angle_d_prot
o_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
o_dihedral_angle_d3.5
o_angle_deg3.2
o_improper_angle_d0.024
o_bond_d0.016
o_bond_d_na
o_bond_d_prot
o_angle_d
o_angle_d_na
o_angle_d_prot
o_angle_deg_na
o_angle_deg_prot
o_dihedral_angle_d_na
o_dihedral_angle_d_prot
o_improper_angle_d_na
o_improper_angle_d_prot
o_mcbond_it
o_mcangle_it
o_scbond_it
o_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2427
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms7

Software

Software
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
CCP4data scaling