2VJY

Pyruvate decarboxylase from Kluyveromyces lactis in complex with the substrate analogue methyl acetylphosphonate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.128120MM CITRATE, 10% PEG2000, 10% PEG6000, 5MM TDP, 5MM MAGNESIUM SULFATE, 1MM DTT, 40MM METHYL ACETYLPHOSPHONATE, PH 6.1, 0.95MG KLPDC/ML, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K
Crystal Properties
Matthews coefficientSolvent content
2.3547.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.76α = 90
b = 135.77β = 103.88
c = 107.26γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2006-12-06MSINGLE 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
12.39999.70.159.64.41004261
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)
12.32.3499.90.612.3

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 2G1I2.320.1999345100699.80.1540.1540.225RANDOM26.26
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]
0.020.690.62-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.646
r_dihedral_angle_4_deg23.335
r_dihedral_angle_3_deg17.718
r_dihedral_angle_1_deg7.218
r_scangle_it4.255
r_scbond_it2.828
r_mcangle_it2.033
r_angle_refined_deg1.952
r_mcbond_it1.263
r_symmetry_hbond_refined1.027
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.646
r_dihedral_angle_4_deg23.335
r_dihedral_angle_3_deg17.718
r_dihedral_angle_1_deg7.218
r_scangle_it4.255
r_scbond_it2.828
r_mcangle_it2.033
r_angle_refined_deg1.952
r_mcbond_it1.263
r_symmetry_hbond_refined1.027
r_nbtor_refined0.313
r_symmetry_vdw_refined0.274
r_nbd_refined0.227
r_chiral_restr0.167
r_xyhbond_nbd_refined0.155
r_bond_refined_d0.025
r_gen_planes_refined0.008
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 Atoms17344
Nucleic Acid Atoms
Solvent Atoms1048
Heterogen Atoms196

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing