9PWN | pdb_00009pwn

Crystal structure of Fabs 7411 in complex with TREM2 peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelModeller 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629311% w/v PEG 8000, 240 mM ammonium sulfate, 100 mM MES
Crystal Properties
Matthews coefficientSolvent content
2.0239

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.65α = 90
b = 71.76β = 90
c = 105.53γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.000070SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.84099.80.9988.525.2174028
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8594.70.5652.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.838.9633550176695.20.179740.177720.18830.217860.2242RANDOM31.69
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]
0.8-0.11-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.346
r_dihedral_angle_1_deg7.558
r_long_range_B_refined6.794
r_long_range_B_other6.762
r_dihedral_angle_2_deg5.963
r_scangle_other4.933
r_scbond_it3.372
r_scbond_other3.371
r_mcangle_it3.053
r_mcangle_other3.052
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.346
r_dihedral_angle_1_deg7.558
r_long_range_B_refined6.794
r_long_range_B_other6.762
r_dihedral_angle_2_deg5.963
r_scangle_other4.933
r_scbond_it3.372
r_scbond_other3.371
r_mcangle_it3.053
r_mcangle_other3.052
r_mcbond_it2.157
r_mcbond_other2.153
r_angle_refined_deg1.299
r_angle_other_deg0.454
r_chiral_restr0.069
r_gen_planes_refined0.01
r_bond_refined_d0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_4_deg
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 Atoms3352
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction