5UGV

DapB from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52980.2 M lithium sulfate monohydrate, 0.1 M tris pH 8.5, 25% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5852.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.507α = 90
b = 88.566β = 90
c = 77.629γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2016-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.254098.40.060.060.0740.03629.6427944-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.2997.10.6520.6520.7980.3890.7762.13.9

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 REPLACEMENTTHROUGHOUT1YL62.254026507140097.810.166790.164960.19982RANDOM54.517
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]
1.12.41-3.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.086
r_dihedral_angle_4_deg22.877
r_dihedral_angle_3_deg13.428
r_long_range_B_refined7.607
r_long_range_B_other7.606
r_scangle_other5.696
r_dihedral_angle_1_deg5.672
r_angle_other_deg3.766
r_mcangle_other3.665
r_mcangle_it3.663
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.086
r_dihedral_angle_4_deg22.877
r_dihedral_angle_3_deg13.428
r_long_range_B_refined7.607
r_long_range_B_other7.606
r_scangle_other5.696
r_dihedral_angle_1_deg5.672
r_angle_other_deg3.766
r_mcangle_other3.665
r_mcangle_it3.663
r_scbond_it3.617
r_scbond_other3.615
r_mcbond_it2.35
r_mcbond_other2.339
r_angle_refined_deg1.921
r_chiral_restr0.109
r_bond_refined_d0.02
r_gen_planes_other0.015
r_gen_planes_refined0.009
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3579
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing