2VEN

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
2.2846.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.1α = 90
b = 88.3β = 97
c = 56.5γ = 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
122598.80.1711.515.3300313
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)
122.198.40.643.475.4

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 1DKW219.882852815021000.1880.1860.237RANDOM9.75
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]
0.060.380.55-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.779
r_dihedral_angle_4_deg17.222
r_dihedral_angle_3_deg16.347
r_dihedral_angle_1_deg6.994
r_scangle_it2.649
r_scbond_it1.737
r_angle_refined_deg1.45
r_mcangle_it1.078
r_mcbond_it0.649
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.779
r_dihedral_angle_4_deg17.222
r_dihedral_angle_3_deg16.347
r_dihedral_angle_1_deg6.994
r_scangle_it2.649
r_scbond_it1.737
r_angle_refined_deg1.45
r_mcangle_it1.078
r_mcbond_it0.649
r_nbtor_refined0.294
r_nbd_refined0.197
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.152
r_chiral_restr0.108
r_symmetry_hbond_refined0.106
r_bond_refined_d0.015
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 Atoms3559
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing