7MP0

CRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1 IN COMPLEX WITH 1D-MYO-INOSITOL 5-DIPHOSPHATE PENTAKISPHOSPHATE (5-PP IP5)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72810.1 M Bis-tris propane pH 7, 35% 2-Ethoxyethanol, 0.001 M Magnesium acetate, 5 mM 1D-myo-inositol 5-diphosphate pentakisphosphate
Crystal Properties
Matthews coefficientSolvent content
3.9468.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.995α = 90
b = 186.822β = 90
c = 90.539γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.979460SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.65099.80.0810.99918.166.788724
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.761.7720.6110.98

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT7JTB2.649.1484114443199.650.22270.22150.2476RANDOM86.191
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]
2.712.65-5.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.72
r_dihedral_angle_3_deg13.804
r_dihedral_angle_4_deg12.216
r_dihedral_angle_1_deg7.419
r_angle_refined_deg1.227
r_angle_other_deg1.042
r_chiral_restr0.041
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.72
r_dihedral_angle_3_deg13.804
r_dihedral_angle_4_deg12.216
r_dihedral_angle_1_deg7.419
r_angle_refined_deg1.227
r_angle_other_deg1.042
r_chiral_restr0.041
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11500
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms206

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
REFMACphasing