2BYO

Crystal structure of Mycobacterium tuberculosis lipoprotein LppX (Rv2945c)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
181.8 M NACL, 0.1 M ZN-ACETATE, 0.1 M IMIDAZOLE-MALATE, PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.753

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.257α = 90
b = 54.257β = 90
c = 269.983γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.152098.60.0570.057248.41368028.33
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2798.60.1210.1215.75.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONOTHERTHROUGHOUT2.1519.1412239135698.70.1890.1850.224RANDOM53.58
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]
1.450.721.45-2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.886
r_dihedral_angle_4_deg16.746
r_dihedral_angle_3_deg12.585
r_dihedral_angle_1_deg6.377
r_scangle_it2.394
r_scbond_it1.788
r_mcangle_it1.416
r_angle_refined_deg1.268
r_mcbond_it1.187
r_angle_other_deg0.701
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.886
r_dihedral_angle_4_deg16.746
r_dihedral_angle_3_deg12.585
r_dihedral_angle_1_deg6.377
r_scangle_it2.394
r_scbond_it1.788
r_mcangle_it1.416
r_angle_refined_deg1.268
r_mcbond_it1.187
r_angle_other_deg0.701
r_symmetry_hbond_refined0.249
r_nbd_refined0.216
r_symmetry_vdw_refined0.188
r_nbd_other0.183
r_xyhbond_nbd_refined0.175
r_nbtor_refined0.161
r_symmetry_vdw_other0.137
r_nbtor_other0.081
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1346
Nucleic Acid Atoms
Solvent Atoms127
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling