3GMA

Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum co-crystallized with glutaryl-CoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PIX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPco-crystallized with substrate analogon glutaryl-CoA, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
4.0169.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 156.472α = 90
b = 156.472β = 90
c = 141.403γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2008-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.54179

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
12.59470.71198.70.1030.1036.7386.561822
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)
12.592.7391.40.4550.4551.76.18274

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 REPLACEMENTTHROUGHOUT1PIX2.668.526100070099.470.189340.189110.20891RANDOM36.737
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]
-0.3-0.15-0.30.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.809
r_dihedral_angle_4_deg15.597
r_dihedral_angle_3_deg14.35
r_dihedral_angle_1_deg5.476
r_scangle_it1.563
r_angle_refined_deg1.144
r_scbond_it0.945
r_mcangle_it0.825
r_mcbond_it0.476
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.809
r_dihedral_angle_4_deg15.597
r_dihedral_angle_3_deg14.35
r_dihedral_angle_1_deg5.476
r_scangle_it1.563
r_angle_refined_deg1.144
r_scbond_it0.945
r_mcangle_it0.825
r_mcbond_it0.476
r_nbtor_refined0.302
r_nbd_refined0.192
r_symmetry_vdw_refined0.168
r_xyhbond_nbd_refined0.109
r_symmetry_hbond_refined0.097
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms8692
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms112

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection