5V68

Crystal structure of cell division protein FtsZ from Mycobacterium tuberculosis bounded via the T9 loop


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q1Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.1M sodium citrate pH 5.6, 0.3M ammonium acetate, 15% PEG 4000. Protein concentration 3mg/ml. Incubated with 5mM SB-P17-A20
Crystal Properties
Matthews coefficientSolvent content
3.1360.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.11α = 90
b = 180.85β = 90
c = 220.16γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.0781NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
13.4655.0596.40.0890.0530.9979.33.337287
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.463.5597.30.6140.3660.7351.83.3

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 REPLACEMENTTHROUGHOUT2Q1Y3.4655.0535388188195.50.246360.242950.3086RANDOM119.98
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]
-2.083.73-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.137
r_dihedral_angle_3_deg18.634
r_long_range_B_refined16.862
r_long_range_B_other16.86
r_dihedral_angle_4_deg15.293
r_mcangle_it12.06
r_mcangle_other12.059
r_scangle_other10.911
r_mcbond_it7.424
r_mcbond_other7.424
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.137
r_dihedral_angle_3_deg18.634
r_long_range_B_refined16.862
r_long_range_B_other16.86
r_dihedral_angle_4_deg15.293
r_mcangle_it12.06
r_mcangle_other12.059
r_scangle_other10.911
r_mcbond_it7.424
r_mcbond_other7.424
r_dihedral_angle_1_deg7.135
r_scbond_it6.43
r_scbond_other6.42
r_angle_refined_deg1.47
r_angle_other_deg1.031
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms11874
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIXmodel building
PHENIXrefinement
xia2data reduction