2VEI

Structure-based enzyme engineering efforts with an inactive monomeric TIM variant: the importance of a single point mutation for generating an active site with suitable binding properties


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DKWPDB ENTRY 1DKW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.1 M TRIS/HCL PH 8.5, 1.9 M MGSO4
Crystal Properties
Matthews coefficientSolvent content
2.5852.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.24α = 90
b = 52.59β = 119.04
c = 92.38γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHPROPHYSICS XRM-2162001-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

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
11.892599.30.0618.43.8614273
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)
11.891.9599.70.157.323.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1DKW1.8918.855835530721000.1680.1660.215RANDOM12.99
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]
-0.220.10.35-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.632
r_dihedral_angle_4_deg16.473
r_dihedral_angle_3_deg13.493
r_dihedral_angle_1_deg5.85
r_scangle_it3.168
r_scbond_it2.029
r_mcangle_it1.203
r_mcbond_it0.73
r_nbtor_refined0.303
r_symmetry_hbond_refined0.284
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.632
r_dihedral_angle_4_deg16.473
r_dihedral_angle_3_deg13.493
r_dihedral_angle_1_deg5.85
r_scangle_it3.168
r_scbond_it2.029
r_mcangle_it1.203
r_mcbond_it0.73
r_nbtor_refined0.303
r_symmetry_hbond_refined0.284
r_nbd_refined0.205
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.143
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_refined_deg
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5433
Nucleic Acid Atoms
Solvent Atoms776
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing