2W93

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VK8PDB ENTRY 2VK8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.3528115 MM CITRATE, 1.67 MM MES, 300 MM PYRUVAMIDE, 1.67 MM TDP, 1.67 MM MAGNESIUM SUFATE, 1.67 MM DTT, 11.25% PEG 2000, 11.25% PEG 6000, 1.1 MG SCPDC/ML, PH 6.35, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE, 281 K
Crystal Properties
Matthews coefficientSolvent content
2.2144.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.05α = 89.23
b = 79.22β = 73.32
c = 109.09γ = 62.43
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2007-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X12EMBL/DESY, HAMBURGX12

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
11.699960.04191.92605852
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)
11.61.6391.60.392

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 2VK81.6103.72594661070960.1810.1810.213RANDOM24.01
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]
0.17-0.110.64-0.1-0.95-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.675
r_dihedral_angle_4_deg17.097
r_dihedral_angle_3_deg13.493
r_dihedral_angle_1_deg5.667
r_scangle_it2.766
r_scbond_it1.832
r_angle_refined_deg1.345
r_mcangle_it1.204
r_mcbond_it0.698
r_chiral_restr0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.675
r_dihedral_angle_4_deg17.097
r_dihedral_angle_3_deg13.493
r_dihedral_angle_1_deg5.667
r_scangle_it2.766
r_scbond_it1.832
r_angle_refined_deg1.345
r_mcangle_it1.204
r_mcbond_it0.698
r_chiral_restr0.49
r_nbtor_refined0.311
r_bond_refined_d0.235
r_nbd_refined0.218
r_symmetry_vdw_refined0.201
r_symmetry_hbond_refined0.141
r_xyhbond_nbd_refined0.125
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 Atoms17113
Nucleic Acid Atoms
Solvent Atoms1413
Heterogen Atoms164

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing