2GKN | pdb_00002gkn

Crystal structure of Mycobacterium tuberculosis trHbN, GlnE11Val mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.6277di-potassium hydrogen phosphate + sodium dihydrogen phosphate 1.8 M, pH 7.6, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2144.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.034α = 90
b = 62.388β = 90
c = 90.974γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2005-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

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
12.151.4373.20.1432.51063110631
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)
2.12.2164.70.6471.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.151.43106311063157172.050.212010.212010.208340.220.285410.29RANDOM21.359
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]
-0.351.4-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.645
r_dihedral_angle_3_deg14.068
r_dihedral_angle_4_deg12.691
r_scangle_it4.957
r_dihedral_angle_1_deg4.668
r_scbond_it3.546
r_mcangle_it2.2
r_mcbond_it1.327
r_angle_refined_deg1.13
r_nbtor_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.645
r_dihedral_angle_3_deg14.068
r_dihedral_angle_4_deg12.691
r_scangle_it4.957
r_dihedral_angle_1_deg4.668
r_scbond_it3.546
r_mcangle_it2.2
r_mcbond_it1.327
r_angle_refined_deg1.13
r_nbtor_refined0.293
r_symmetry_hbond_refined0.251
r_nbd_refined0.191
r_symmetry_vdw_refined0.172
r_xyhbond_nbd_refined0.13
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms1900
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms91

Software

Software
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement