6BWC

X-ray structure of Pen from Bacillus thuringiensis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52772.2-2.5 M ammonium sulfate, 100 mM HEPES, 5 mM UDP-GlcNAc
Crystal Properties
Matthews coefficientSolvent content
2.5752.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.524α = 90
b = 141.876β = 111.66
c = 93.244γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352016-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.786.6690.70.0940.0949.8555673
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)
12.72.884.10.3010.3012.42.2

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 REPLACEMENTTHROUGHOUT2gn42.73052775289690.680.203950.201330.2512RANDOM26.501
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]
-1.72-0.923.28-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.517
r_dihedral_angle_3_deg20.374
r_dihedral_angle_4_deg15.544
r_dihedral_angle_1_deg7.572
r_long_range_B_refined4.033
r_long_range_B_other4.008
r_mcangle_it2.384
r_mcangle_other2.384
r_scangle_other2.218
r_angle_refined_deg1.733
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.517
r_dihedral_angle_3_deg20.374
r_dihedral_angle_4_deg15.544
r_dihedral_angle_1_deg7.572
r_long_range_B_refined4.033
r_long_range_B_other4.008
r_mcangle_it2.384
r_mcangle_other2.384
r_scangle_other2.218
r_angle_refined_deg1.733
r_mcbond_it1.399
r_mcbond_other1.399
r_scbond_it1.283
r_scbond_other1.275
r_angle_other_deg0.998
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms15321
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms547

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing