2FK8

Crystal structure of Hma (MmaA4) from Mycobacterium tuberculosis complexed with S-adenosylmethionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FK7pdb entry 2FK7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52854-28% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K
Crystal Properties
Matthews coefficientSolvent content
2.6753.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.779α = 90
b = 56.779β = 90
c = 199.035γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Toroidal mirror2004-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.979171ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
123097.70.0854.83.9255492554930.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1188.10.2232.93.23284

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2FK72302418424184130297.50.182140.182140.179280.23889RANDOM36.975
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]
0.520.260.52-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.269
r_dihedral_angle_4_deg21.181
r_dihedral_angle_3_deg13.197
r_dihedral_angle_1_deg5.55
r_scangle_it3.916
r_scbond_it2.566
r_angle_refined_deg1.539
r_mcangle_it1.489
r_mcbond_it0.975
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.269
r_dihedral_angle_4_deg21.181
r_dihedral_angle_3_deg13.197
r_dihedral_angle_1_deg5.55
r_scangle_it3.916
r_scbond_it2.566
r_angle_refined_deg1.539
r_mcangle_it1.489
r_mcbond_it0.975
r_nbtor_refined0.31
r_symmetry_hbond_refined0.202
r_nbd_refined0.201
r_symmetry_vdw_refined0.183
r_xyhbond_nbd_refined0.17
r_chiral_restr0.114
r_bond_refined_d0.016
r_gen_planes_refined0.006
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 Atoms2236
Nucleic Acid Atoms
Solvent Atoms153
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing