3GF3

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3748.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.36α = 90
b = 144.36β = 90
c = 167.15γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2008-08-08MSINGLE 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
11.7537.34997.90.0460.04610.3913.960672
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)
11.751.8499.70.2620.2622.93.78956

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 REPLACEMENTTHROUGHOUT1PIX1.7536.1560667242697.660.1630.1630.176RANDOM23.183
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]
-0.99-1.152.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.685
r_dihedral_angle_4_deg16.292
r_dihedral_angle_3_deg11.577
r_dihedral_angle_1_deg6.974
r_scangle_it2.245
r_scbond_it1.405
r_angle_refined_deg1.173
r_mcangle_it0.884
r_mcbond_it0.537
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.685
r_dihedral_angle_4_deg16.292
r_dihedral_angle_3_deg11.577
r_dihedral_angle_1_deg6.974
r_scangle_it2.245
r_scbond_it1.405
r_angle_refined_deg1.173
r_mcangle_it0.884
r_mcbond_it0.537
r_nbtor_refined0.304
r_nbd_refined0.191
r_xyhbond_nbd_refined0.179
r_symmetry_vdw_refined0.159
r_symmetry_hbond_refined0.135
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4346
Nucleic Acid Atoms
Solvent Atoms465
Heterogen Atoms54

Software

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