4M65

In situ thermolysin crystallized on a MiTeGen micromesh with asparagine ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TLNPDB ENTRY 4TLN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1In situ crystallization on micromesh7.52901.45M calcium chloride, 45% DMSO, 50mM TRIS pH 7.5, In situ crystallization on micromesh, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.3347.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.831α = 90
b = 92.831β = 90
c = 129.171γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102013-08-04MSINGLE WAVELENGTH
21PIXELDECTRIS PILATUS 6M
31CCDADSC QUANTUM 315
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12C1.1NSLSX12C
2SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25
3SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.631.5998.10.04858.428.2435774303521

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 4TLN1.631.5924303540851216798.170.13160.13160.130080.15928RANDOM16.678
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]
-0.43-0.43-0.431.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.072
r_dihedral_angle_4_deg17.971
r_dihedral_angle_3_deg12.666
r_long_range_B_refined7.363
r_long_range_B_other6.555
r_dihedral_angle_1_deg5.829
r_scangle_other4.157
r_scbond_it2.983
r_scbond_other2.983
r_angle_refined_deg2.559
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.072
r_dihedral_angle_4_deg17.971
r_dihedral_angle_3_deg12.666
r_long_range_B_refined7.363
r_long_range_B_other6.555
r_dihedral_angle_1_deg5.829
r_scangle_other4.157
r_scbond_it2.983
r_scbond_other2.983
r_angle_refined_deg2.559
r_mcangle_it2.004
r_mcangle_other2.004
r_mcbond_it1.518
r_mcbond_other1.517
r_angle_other_deg1.128
r_chiral_restr0.164
r_bond_refined_d0.029
r_gen_planes_refined0.014
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2431
Nucleic Acid Atoms
Solvent Atoms460
Heterogen Atoms61

Software

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