7NSX

Drosophila PGRP-LB wild-type


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1M HEPES pH7.0, 30% v/v Jeffamine ED-2003
Crystal Properties
Matthews coefficientSolvent content
1.6726.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.869α = 90
b = 70.546β = 90
c = 112.828γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-09-27MSINGLE 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
11.9112.8399.80.1330.1530.0730.9938.57.912942
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)
11.91.941.1971.3940.6990.5627.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1OHT1.956.4781288368099.6670.1820.17990.212827.154
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]
-0.3090.2230.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.274
r_dihedral_angle_4_deg16.653
r_dihedral_angle_3_deg13.199
r_dihedral_angle_1_deg6.912
r_lrange_it5.566
r_lrange_other5.562
r_scangle_it4.431
r_scangle_other4.403
r_mcangle_other3.125
r_mcangle_it3.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.274
r_dihedral_angle_4_deg16.653
r_dihedral_angle_3_deg13.199
r_dihedral_angle_1_deg6.912
r_lrange_it5.566
r_lrange_other5.562
r_scangle_it4.431
r_scangle_other4.403
r_mcangle_other3.125
r_mcangle_it3.116
r_scbond_it2.949
r_scbond_other2.914
r_mcbond_it2.224
r_mcbond_other2.207
r_angle_refined_deg1.597
r_angle_other_deg1.368
r_symmetry_nbd_refined0.239
r_nbd_refined0.203
r_nbd_other0.203
r_symmetry_nbd_other0.185
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.141
r_symmetry_xyhbond_nbd_refined0.119
r_symmetry_nbtor_other0.077
r_chiral_restr0.074
r_metal_ion_refined0.022
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1334
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms1

Software

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