3GF7

Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum apoprotein


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3647.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.05α = 90
b = 143.53β = 90
c = 167.52γ = 90
Symmetry
Space GroupF 2 2 2

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
12.432.98799.90.0740.0749.076.124154
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)
12.42.531000.3340.3342.36.23477

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 REPLACEMENTTHROUGHOUT1PIX2.432.4824153100299.810.1870.1850.225RANDOM31.586
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]
-2.050.551.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.972
r_dihedral_angle_4_deg13.466
r_dihedral_angle_3_deg13.163
r_dihedral_angle_1_deg6.66
r_scangle_it1.585
r_angle_refined_deg1.095
r_scbond_it0.988
r_mcangle_it0.831
r_mcbond_it0.481
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.972
r_dihedral_angle_4_deg13.466
r_dihedral_angle_3_deg13.163
r_dihedral_angle_1_deg6.66
r_scangle_it1.585
r_angle_refined_deg1.095
r_scbond_it0.988
r_mcangle_it0.831
r_mcbond_it0.481
r_nbtor_refined0.307
r_nbd_refined0.199
r_symmetry_vdw_refined0.172
r_symmetry_hbond_refined0.143
r_xyhbond_nbd_refined0.131
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4202
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms5

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction