3PMD

Crystal structure of the sporulation inhibitor pXO1-118 from Bacillus anthracis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.42985% PEG1000, 40% PEG400, 0.1 M TrisHCl, pH 5.4, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2244.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.223α = 90
b = 89.223β = 90
c = 35.819γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9781SSRLBL9-2

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
11.765098.90.03855.116351-3
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)
1.761.82960.276

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 DIFFRACTIONSADTHROUGHOUT1.76501561783099.880.18020.177920.22316RANDOM28.056
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]
-0.53-0.27-0.530.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.068
r_dihedral_angle_4_deg20.496
r_dihedral_angle_3_deg12.402
r_scangle_it7.782
r_scbond_it5.176
r_dihedral_angle_1_deg3.993
r_mcangle_it2.991
r_mcbond_it1.774
r_angle_other_deg1.612
r_angle_refined_deg1.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.068
r_dihedral_angle_4_deg20.496
r_dihedral_angle_3_deg12.402
r_scangle_it7.782
r_scbond_it5.176
r_dihedral_angle_1_deg3.993
r_mcangle_it2.991
r_mcbond_it1.774
r_angle_other_deg1.612
r_angle_refined_deg1.069
r_mcbond_other0.644
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1306
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms14

Software

Software
Software NamePurpose
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling