9HGH | pdb_00009hgh

MyD88 peptide_1 bound to SPOP MATH domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KPI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29112.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M diethyleneglycol, 0.03 M triethyleneglycol, 0.03 M tetraethyleneglycol, 0.03 M pentaethyleneglycol, 0.1 M bicine/Trizma base pH 8.5
Crystal Properties
Matthews coefficientSolvent content
1.9436.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40α = 90
b = 57.29β = 90
c = 60.97γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X CdTe 9M2022-04-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.99987DiamondI24

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
11.933.4499.40.999.85.811453
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)
11.91.9797.80.76

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)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)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.933.441.361145154799.380.17580.1730.17210.23220.232522.5
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d6.1476
f_angle_d1.1321
f_chiral_restr0.0606
f_bond_d0.011
f_plane_restr0.0101
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1219
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing
Cootmodel building