7MP1

CRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1 IN COMPLEX WITH 1,5-DI-METHYLENEBISPHOSPHONATE INOSITOL TETRAKISPHOSPHATE (1,5-PCP-IP4)


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 7.0, 35% 2-Ethoxyethanol, 0.001 M Magnesium acetate, 5 mM 1,5-DI-METHYLENEBISPHOSPHONATE INOSITOL TETRAKISPHOSPHATE (1,5-PCP-IP4)
Crystal Properties
Matthews coefficientSolvent content
3.9568.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.467α = 90
b = 187.229β = 90
c = 90.743γ = 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
12.665099.90.1440.99916.0713.68308777.3
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)
12.662.8299.82.770.5320.89

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 SYNTHESISTHROUGHOUT7JTB2.6649.2378647413399.540.22150.22010.2485RANDOM86.133
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]
2.531.84-4.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.445
r_dihedral_angle_3_deg14.022
r_dihedral_angle_4_deg13.136
r_dihedral_angle_1_deg7.617
r_angle_refined_deg1.235
r_angle_other_deg1.049
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_deg31.445
r_dihedral_angle_3_deg14.022
r_dihedral_angle_4_deg13.136
r_dihedral_angle_1_deg7.617
r_angle_refined_deg1.235
r_angle_other_deg1.049
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 Atoms11514
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms220

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
REFMACphasing