7MP1 | pdb_00007mp1

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)
Type	Source	Accession Code	Details
experimental model	PDB	7JTB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	281	0.1 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 coefficient	Solvent content
3.95	68.83

Crystal Data

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

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2020-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.979460	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.66	50	99.9	0.144	0.999	16.07	13.6		83087			77.3

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)	Redundancy	Number Unique Reflections (All)
1	2.66	2.82	99.8		2.77	0.532	0.89

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	7JTB	2.66	49.23	78647	4133	99.54	0.2215	0.2201	0.23	0.2485	0.25	RANDOM	86.133

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]
2.53			1.84		-4.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.445
r_dihedral_angle_3_deg	14.022
r_dihedral_angle_4_deg	13.136
r_dihedral_angle_1_deg	7.617
r_angle_refined_deg	1.235
r_angle_other_deg	1.049
r_chiral_restr	0.041
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.445
r_dihedral_angle_3_deg	14.022
r_dihedral_angle_4_deg	13.136
r_dihedral_angle_1_deg	7.617
r_angle_refined_deg	1.235
r_angle_other_deg	1.049
r_chiral_restr	0.041
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11514
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	220

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.