8R1N

Pim1 in complex with 4-(4-hydroxyphenethyl)benzoic acid and Pimtide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NDT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7291.15100 mM bis-tris-propane (pH 7.0), 10% ethylene glycol, 0.3% DMSO, 20% PEG3350, 200 mM Mg(OAc)2
Crystal Properties
Matthews coefficientSolvent content
3.159.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.115α = 90
b = 97.115β = 90
c = 79.938γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
12.2148.5699.60.9928.111.32157635.55
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)
12.212.220.95

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.2136.11.3821568107899.60.16280.16130.191939.89
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_d12.0937
f_angle_d0.7729
f_chiral_restr0.0518
f_plane_restr0.0082
f_bond_d0.0068
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2217
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms18

Software

Software
Software NamePurpose
MxCuBEdata collection
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building