2XT6

Crystal structure of Mycobacterium smegmatis alpha-ketoglutarate decarboxylase homodimer (orthorhombic form)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1739% MPD, 100 MM HEPES, PH 7.0, 200 MM NACL
Crystal Properties
Matthews coefficientSolvent content
3.362.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.99α = 90
b = 247.72β = 90
c = 79.98γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCDKIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS2009-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

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
12.748299.30.0710.33.5798352.475.02
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)
12.742.8997.50.422.43.2

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 2XT92.7440.1279534401799.130.18740.18540.2236RANDOM70.04
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]
25.4159-9.113-16.303
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.11
t_other_torsion2.95
t_angle_deg1.09
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_torsion3.11
t_other_torsion2.95
t_angle_deg1.09
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 Atoms15727
Nucleic Acid Atoms
Solvent Atoms119
Heterogen Atoms56

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing