2VK4

Crystal structure of pyruvate decarboxylase from Kluyveromyces lactis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2G1IPDB ENTRY 2G1I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.4528150MM MES, 1MM DTT, 5MM TDP, 5MM MAGNESIUM SULFATE, 10% PEG 2000, 10% PEG 8000, 2MG KLPDC/ML, PH 6.45, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K
Crystal Properties
Matthews coefficientSolvent content
2.5952.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.709α = 90
b = 203.175β = 91.81
c = 79.815γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

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
11.9548.4586.30.111.54.31553151
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)
11.952.0680.60.512.5

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 2G1I1.9548.4514744677841000.180.1780.23RANDOM22.08
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]
-0.06-0.060.26-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.346
r_dihedral_angle_4_deg21.703
r_dihedral_angle_3_deg16.696
r_dihedral_angle_1_deg6.596
r_scangle_it3.772
r_scbond_it2.512
r_angle_refined_deg1.85
r_mcangle_it1.588
r_mcbond_it0.929
r_chiral_restr0.441
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.346
r_dihedral_angle_4_deg21.703
r_dihedral_angle_3_deg16.696
r_dihedral_angle_1_deg6.596
r_scangle_it3.772
r_scbond_it2.512
r_angle_refined_deg1.85
r_mcangle_it1.588
r_mcbond_it0.929
r_chiral_restr0.441
r_nbtor_refined0.308
r_nbd_refined0.223
r_symmetry_vdw_refined0.22
r_xyhbond_nbd_refined0.183
r_symmetry_hbond_refined0.144
r_bond_refined_d0.019
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 Atoms17227
Nucleic Acid Atoms
Solvent Atoms1319
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing