2VEM

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
15.520% PEG6000, 2,5% T-BUTANOL, 0.1 M CITRIC ACID PH 5,5
Crystal Properties
Matthews coefficientSolvent content
2.2344.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.8α = 90
b = 86.9β = 97.2
c = 56.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
12.22599.80.1414.367.6222623
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)
12.22.31000.623.637.6

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 1DKW2.219.662114811141000.1960.1930.247RANDOM22.51
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]
-0.170.150.47-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.778
r_dihedral_angle_3_deg17.857
r_dihedral_angle_4_deg12.813
r_dihedral_angle_1_deg6.303
r_scangle_it2.585
r_scbond_it1.646
r_angle_refined_deg1.405
r_mcangle_it1.103
r_mcbond_it0.65
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.778
r_dihedral_angle_3_deg17.857
r_dihedral_angle_4_deg12.813
r_dihedral_angle_1_deg6.303
r_scangle_it2.585
r_scbond_it1.646
r_angle_refined_deg1.405
r_mcangle_it1.103
r_mcbond_it0.65
r_nbtor_refined0.3
r_nbd_refined0.209
r_xyhbond_nbd_refined0.162
r_symmetry_vdw_refined0.161
r_chiral_restr0.089
r_symmetry_hbond_refined0.077
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
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 Atoms3593
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing