5HL3

Crystal structure of Listeria monocytogenes InlP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931/1 ratio of InlP 8.5 mg/ml in 10 mMTrisHCl pH 8.3, 1 mM TCEP and 0.2 M Calcium Chloride, 0.1 M TrisHCl pH 8, 20%(w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.9858.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.883α = 90
b = 72.883β = 90
c = 179.449γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.43099.80.0790.07930.25.6180423
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)
11.41.421000.6532.65.3

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 DIFFRACTIONSADTHROUGHOUT1.43090409463599.750.160640.159870.176RANDOM16.278
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]
0.510.51-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.377
r_dihedral_angle_4_deg18.098
r_dihedral_angle_3_deg10.345
r_long_range_B_refined9.011
r_long_range_B_other8.583
r_dihedral_angle_1_deg5.363
r_angle_refined_deg1.507
r_scangle_other0.939
r_angle_other_deg0.883
r_scbond_it0.671
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.377
r_dihedral_angle_4_deg18.098
r_dihedral_angle_3_deg10.345
r_long_range_B_refined9.011
r_long_range_B_other8.583
r_dihedral_angle_1_deg5.363
r_angle_refined_deg1.507
r_scangle_other0.939
r_angle_other_deg0.883
r_scbond_it0.671
r_scbond_other0.671
r_mcangle_it0.429
r_mcangle_other0.429
r_mcbond_it0.246
r_mcbond_other0.245
r_chiral_restr0.095
r_gen_planes_refined0.023
r_gen_planes_other0.019
r_bond_refined_d0.011
r_bond_other_d0.001
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 Atoms2779
Nucleic Acid Atoms
Solvent Atoms812
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
BLU-MAXdata collection