2FK7

Crystal structure of Hma (MmaA4) from Mycobacterium tuberculosis, apo-form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KP9pdb entry 1KP9

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
2.7655.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.715α = 90
b = 56.715β = 90
c = 206.22γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHToroidal mirror2004-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.931000ESRFID14-3

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
12.144.397.50.13.89.7227762277642.3
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)
12.12.211000.1863.7103315

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 1KP92.1302153521535117397.050.197340.197340.195460.23226RANDOM65.44
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]
0.550.270.55-0.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.047
r_dihedral_angle_4_deg23.723
r_dihedral_angle_3_deg13.795
r_dihedral_angle_1_deg5.854
r_scangle_it3.95
r_scbond_it2.788
r_angle_refined_deg1.736
r_mcangle_it1.636
r_mcbond_it1.176
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.047
r_dihedral_angle_4_deg23.723
r_dihedral_angle_3_deg13.795
r_dihedral_angle_1_deg5.854
r_scangle_it3.95
r_scbond_it2.788
r_angle_refined_deg1.736
r_mcangle_it1.636
r_mcbond_it1.176
r_nbtor_refined0.317
r_symmetry_hbond_refined0.235
r_nbd_refined0.211
r_chiral_restr0.132
r_xyhbond_nbd_refined0.123
r_symmetry_vdw_refined0.111
r_bond_refined_d0.021
r_gen_planes_refined0.008
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 Atoms2218
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing