3GLM

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPco-crystallized with crotonyl-CoA, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2645.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.5α = 90
b = 167.45β = 89.98
c = 138.11γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.80150EMBL/DESY, HAMBURGX13

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
12.536.76199.60.0970.0976.0552.721289379234
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)
12.52.6498.90.4640.4641.12.411510

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.536.767825197799.570.193840.193370.23006RANDOM35.207
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]
-0.120.640.73-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.727
r_dihedral_angle_4_deg16.92
r_dihedral_angle_3_deg14.326
r_dihedral_angle_1_deg5.682
r_scangle_it1.646
r_angle_refined_deg1.201
r_scbond_it1.027
r_mcangle_it0.769
r_mcbond_it0.452
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.727
r_dihedral_angle_4_deg16.92
r_dihedral_angle_3_deg14.326
r_dihedral_angle_1_deg5.682
r_scangle_it1.646
r_angle_refined_deg1.201
r_scbond_it1.027
r_mcangle_it0.769
r_mcbond_it0.452
r_nbtor_refined0.309
r_nbd_refined0.204
r_symmetry_vdw_refined0.192
r_xyhbond_nbd_refined0.132
r_symmetry_hbond_refined0.126
r_chiral_restr0.083
r_bond_refined_d0.009
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 Atoms17299
Nucleic Acid Atoms
Solvent Atoms627
Heterogen Atoms216

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction