2YIC

Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase (triclinic form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XT9PDB ENTRY 2XT9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1746.5% MPD, 100 MM HEPES, PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.7455.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.539α = 99.48
b = 83.244β = 99.06
c = 158.61γ = 101.25
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL FOCUSING MIRROR2009-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.9649.595.20.098.72.9263780223.55
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.962.0791.50.442.22.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XT91.9639.22637381322895.190.18960.18840.2108RANDOM28.82
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]
-2.9185-0.27841.18460.32110.89392.5975
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.47
t_other_torsion2.63
t_angle_deg0.98
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.47
t_other_torsion2.63
t_angle_deg0.98
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25015
Nucleic Acid Atoms
Solvent Atoms1221
Heterogen Atoms112

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing