5IE6

Crystal structure of a lactonase mutant in complex with substrate b


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WZL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529824% PEG 2000 MME, 0.1M Bis-Tris
Crystal Properties
Matthews coefficientSolvent content
2.9157.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.043α = 90
b = 86.043β = 90
c = 470.111γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B10.97622NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.672598.30.0450.0490.02116.15.930272
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.672.7797.40.1536

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 REPLACEMENTTHROUGHOUT3WZL2.6724.9428626151698.160.22390.220990.27931RANDOM44.592
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]
2.191.12.19-7.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.33
r_dihedral_angle_3_deg19.765
r_dihedral_angle_4_deg17.869
r_long_range_B_refined8.971
r_long_range_B_other8.97
r_dihedral_angle_1_deg8.934
r_scangle_other6.974
r_mcangle_it6.328
r_mcangle_other6.327
r_scbond_it4.852
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.33
r_dihedral_angle_3_deg19.765
r_dihedral_angle_4_deg17.869
r_long_range_B_refined8.971
r_long_range_B_other8.97
r_dihedral_angle_1_deg8.934
r_scangle_other6.974
r_mcangle_it6.328
r_mcangle_other6.327
r_scbond_it4.852
r_scbond_other4.848
r_mcbond_it4.463
r_mcbond_other4.463
r_angle_refined_deg1.529
r_angle_other_deg0.969
r_chiral_restr0.106
r_gen_planes_refined0.019
r_bond_refined_d0.01
r_gen_planes_other0.009
r_bond_other_d0.003
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 Atoms5028
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction