2XWN

Crystal structure of IspD from Mycobacterium tuberculosis in complex with CTP and Mg


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293SITTING-DROP VAPOR-DIFFUSION METHOD AT 293 K. DROPS WITH 300 NANOLITERS PROTEIN SOLUTION (PROTEIN AT 10 MG/ML IN 20 MM BIS-TRIS-PROPANE, PH 6.5, 0.1 M NACL WITH 10 MM CTP AND 10 MM MGCL2) AND 300 NANOLITERS SCREENING/RESERVOIR SOLUTION (10% (W/V) PEG 20, 000, 20% (V/V) MONOMETHYL ETHER PEG 550, 0.03 M CACL2, 0.03M MGCL2, AND 0.1 M BICINE/TRIZMA BASE, PH 8.5)
Crystal Properties
Matthews coefficientSolvent content
2.5151.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.06α = 90
b = 82.25β = 90
c = 133.24γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC CCD2010-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.94299.20.1316.27.111201
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)
12.92.9898.90.4947.3

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.941.83106415601000.210650.208330.25337RANDOM33.107
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]
3.32-1.09-2.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.33
r_dihedral_angle_4_deg21.807
r_dihedral_angle_3_deg18.268
r_dihedral_angle_1_deg5.992
r_angle_refined_deg1.344
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.33
r_dihedral_angle_4_deg21.807
r_dihedral_angle_3_deg18.268
r_dihedral_angle_1_deg5.992
r_angle_refined_deg1.344
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms3287
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing