7NT0

Drosophila PGRP-LB Y78F mutant in complex with tracheal cytotoxin (TCT)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OHT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529330% v/v 2-Propanol, 100 mM Tris base HCl pH 8.5, 30% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0941.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.587α = 92.113
b = 52.167β = 105.123
c = 55.579γ = 111.513
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.969DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.853.0797.70.0840.0980.050.99811.96.934852
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.840.4780.560.2890.8916.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1OHT1.853.06734851176097.7420.1460.14470.179819.093
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]
0.6590.031-0.4310.125-0.47-0.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.466
r_dihedral_angle_3_deg11.766
r_dihedral_angle_4_deg11.686
r_dihedral_angle_1_deg7.175
r_lrange_it5.587
r_lrange_other5.555
r_scangle_it4.383
r_scangle_other4.382
r_scbond_it2.907
r_scbond_other2.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.466
r_dihedral_angle_3_deg11.766
r_dihedral_angle_4_deg11.686
r_dihedral_angle_1_deg7.175
r_lrange_it5.587
r_lrange_other5.555
r_scangle_it4.383
r_scangle_other4.382
r_scbond_it2.907
r_scbond_other2.906
r_mcangle_it2.567
r_mcangle_other2.566
r_mcbond_it1.911
r_mcbond_other1.911
r_angle_refined_deg1.684
r_angle_other_deg1.479
r_symmetry_nbd_refined0.333
r_nbd_refined0.213
r_nbd_other0.179
r_symmetry_nbd_other0.178
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.171
r_symmetry_xyhbond_nbd_refined0.141
r_symmetry_nbtor_other0.084
r_chiral_restr0.083
r_symmetry_xyhbond_nbd_other0.061
r_ncsr_local_group_10.051
r_metal_ion_refined0.043
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2625
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata reduction
DIALSdata processing
Cootmodel building
GDAdata collection
Aimlessdata scaling
PHASERphasing