2VBF

The holostructure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OVMPDB ENTRY 1OVM

Crystallization

Crystal Properties
Matthews coefficientSolvent content
1.934.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.603α = 90
b = 108.421β = 90
c = 146.593γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.656.1792.40.0711.33.8127559618
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)
11.61.6963.80.482.22.7

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 1OVM1.630121047643692.20.1650.1630.2RANDOM14.89
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]
-0.61-0.340.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.851
r_dihedral_angle_4_deg16.469
r_dihedral_angle_3_deg12.333
r_dihedral_angle_1_deg5.557
r_scangle_it2.532
r_scbond_it1.853
r_mcangle_it1.66
r_mcbond_it1.472
r_angle_refined_deg1.207
r_angle_other_deg0.891
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.851
r_dihedral_angle_4_deg16.469
r_dihedral_angle_3_deg12.333
r_dihedral_angle_1_deg5.557
r_scangle_it2.532
r_scbond_it1.853
r_mcangle_it1.66
r_mcbond_it1.472
r_angle_refined_deg1.207
r_angle_other_deg0.891
r_symmetry_vdw_refined0.32
r_nbd_refined0.204
r_symmetry_vdw_other0.183
r_nbd_other0.182
r_nbtor_refined0.173
r_symmetry_hbond_refined0.164
r_xyhbond_nbd_refined0.153
r_nbtor_other0.082
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms8564
Nucleic Acid Atoms
Solvent Atoms1109
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing