3CDK

Crystal structure of the co-expressed succinyl-CoA transferase A and B complex from Bacillus subtilis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M3EPDB entry 1M3E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62890.1M tri-Sodium citrate dihydrate pH 5.6, 20% Isopropanol, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3347.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.337α = 90
b = 70.404β = 106.31
c = 97.996γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirrors2007-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9793APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.5948.399.70.1470.1475.93.52808428084-347.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.592.6994.20.5430.5432.23.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1M3E2.5948.32806928069141799.210.195640.192570.25278RANDOM53.745
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]
-3.03-0.532.070.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.356
r_dihedral_angle_3_deg22.442
r_dihedral_angle_4_deg19.168
r_dihedral_angle_1_deg6.976
r_scangle_it5.569
r_mcangle_it4.414
r_scbond_it3.26
r_mcbond_it2.598
r_angle_refined_deg1.599
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.356
r_dihedral_angle_3_deg22.442
r_dihedral_angle_4_deg19.168
r_dihedral_angle_1_deg6.976
r_scangle_it5.569
r_mcangle_it4.414
r_scbond_it3.26
r_mcbond_it2.598
r_angle_refined_deg1.599
r_nbtor_refined0.319
r_symmetry_vdw_refined0.306
r_nbd_refined0.246
r_xyhbond_nbd_refined0.166
r_symmetry_hbond_refined0.145
r_chiral_restr0.108
r_bond_refined_d0.016
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6605
Nucleic Acid Atoms
Solvent Atoms115
Heterogen Atoms

Software

Software
Software NamePurpose
MOLREPphasing
Cootmodel building
REFMACrefinement
SBC-Collectdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling