6J98

Crystal structure of P8 from Lactobacillus rhamnosus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2900.05M Zinc Acetate dihydrate, 20% PEG3350, 5% n-dodecyl-N, N-dimethylamine-N-oxide
Crystal Properties
Matthews coefficientSolvent content
2.4349.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.86α = 90
b = 40.86β = 90
c = 107.01γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2016-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A0.9738Photon FactoryBL-1A

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
11.5638.1799.70.1114.952012894
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.561.60198.980.60.18

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 DIFFRACTIONSADTHROUGHOUT1.5638.171289469799.710.178620.177620.19622RANDOM16.651
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]
-0.63-0.631.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.153
r_dihedral_angle_4_deg24.23
r_dihedral_angle_3_deg10.293
r_dihedral_angle_1_deg4.709
r_long_range_B_refined4.6
r_long_range_B_other4.536
r_scangle_other3.718
r_scbond_it2.628
r_scbond_other2.624
r_mcangle_other2.392
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.153
r_dihedral_angle_4_deg24.23
r_dihedral_angle_3_deg10.293
r_dihedral_angle_1_deg4.709
r_long_range_B_refined4.6
r_long_range_B_other4.536
r_scangle_other3.718
r_scbond_it2.628
r_scbond_other2.624
r_mcangle_other2.392
r_mcangle_it2.388
r_angle_refined_deg1.781
r_mcbond_it1.648
r_mcbond_other1.6
r_angle_other_deg1.586
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms607
Nucleic Acid Atoms
Solvent Atoms77
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
AutoSolphasing