6EFH

Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyruvamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VK4PDB entry 2VK4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.25281.152 mg/mL KlPDC in 2 mM MES, 18 mM citrate, pH 6.25, 4 mM thiamine diphosphate, 4 mM magnesium sulfate, 2 mM DTT, 1:1 with mother liquor (18-24% w/v PEG2000/PEG6000), ~25 days at 8 degrees C, soaked for 50 seconds in 2 uL mother liquor + 2 uL 90% v/v PEG400, 200 mM pyruvamide prior to flash freezing
Crystal Properties
Matthews coefficientSolvent content
3.2261.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 172.765α = 90
b = 172.765β = 90
c = 210.083γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42007-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.93300ESRFID14-2

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
12.9955.61000.333914.43227925.68
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)
12.993.051001.7971.614.7

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 2VK42.9955.63122310551000.1810.1780.265RANDOM42.52
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]
1.941.94-3.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.609
r_dihedral_angle_4_deg20.327
r_dihedral_angle_3_deg19.268
r_dihedral_angle_1_deg8.406
r_long_range_B_refined7.526
r_long_range_B_other7.526
r_mcangle_it5.17
r_mcangle_other5.169
r_scangle_other4.882
r_mcbond_it3.213
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.609
r_dihedral_angle_4_deg20.327
r_dihedral_angle_3_deg19.268
r_dihedral_angle_1_deg8.406
r_long_range_B_refined7.526
r_long_range_B_other7.526
r_mcangle_it5.17
r_mcangle_other5.169
r_scangle_other4.882
r_mcbond_it3.213
r_mcbond_other3.2
r_scbond_it2.985
r_scbond_other2.985
r_angle_refined_deg1.465
r_angle_other_deg0.859
r_chiral_restr0.064
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8587
Nucleic Acid Atoms
Solvent Atoms41
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing