7NSZ

Drosophila PGRP-LB Y78F mutant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2 M Sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
Crystal Properties
Matthews coefficientSolvent content
1.6927.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.502α = 90
b = 40.502β = 90
c = 338.941γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

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
11.3338.9499.90.0960.0980.0220.99820.831.542802
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)
11.31.320.4430.4780.1760.95513

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-VALUE1OHT1.356.55442582213399.9390.1880.18640.220713.906
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]
0.1470.0730.147-0.476
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.19
r_dihedral_angle_4_deg15.455
r_dihedral_angle_3_deg10.466
r_dihedral_angle_1_deg7.009
r_lrange_it4.116
r_lrange_other4.115
r_scangle_it3.098
r_scangle_other3.096
r_scbond_it2.099
r_scbond_other2.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.19
r_dihedral_angle_4_deg15.455
r_dihedral_angle_3_deg10.466
r_dihedral_angle_1_deg7.009
r_lrange_it4.116
r_lrange_other4.115
r_scangle_it3.098
r_scangle_other3.096
r_scbond_it2.099
r_scbond_other2.099
r_angle_refined_deg1.904
r_mcangle_it1.868
r_mcangle_other1.861
r_angle_other_deg1.524
r_mcbond_it1.288
r_mcbond_other1.277
r_nbd_other0.26
r_symmetry_nbd_refined0.231
r_nbd_refined0.22
r_symmetry_nbd_other0.193
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.132
r_symmetry_xyhbond_nbd_refined0.131
r_chiral_restr0.095
r_symmetry_nbtor_other0.085
r_symmetry_metal_ion_refined0.063
r_bond_refined_d0.014
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1337
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms17

Software

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