2VEK

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
2.2445.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.96α = 90
b = 87.22β = 97.5
c = 56.48γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
11.62597.60.129.994.2567663
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)
11.61.796.90.413.274.3

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 1DKW1.619.745392528391000.1670.1660.193RANDOM18.76
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]
0.420.510.18-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.583
r_dihedral_angle_4_deg16.512
r_dihedral_angle_3_deg12.756
r_dihedral_angle_1_deg5.921
r_scangle_it3.727
r_scbond_it2.376
r_angle_refined_deg1.437
r_mcangle_it1.389
r_mcbond_it0.904
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.583
r_dihedral_angle_4_deg16.512
r_dihedral_angle_3_deg12.756
r_dihedral_angle_1_deg5.921
r_scangle_it3.727
r_scbond_it2.376
r_angle_refined_deg1.437
r_mcangle_it1.389
r_mcbond_it0.904
r_nbtor_refined0.305
r_symmetry_hbond_refined0.265
r_nbd_refined0.21
r_symmetry_vdw_refined0.207
r_xyhbond_nbd_refined0.123
r_chiral_restr0.106
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 Atoms3609
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing