6X25 | pdb_00006x25

CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AFTER ADDITION OF INOSITOL 1,3,4-TRISPHOSPHATE AND LITHIUM AT 3.2 ANGSTROM RESOLUTION

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1INP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.25	293	Tetragonal shaped crystals amenable to diffraction studies were grown by the hanging drop vapor diffusion method on silanized glass covers slips at 20 C and grew with dimensions routinely exceeding 0.1 x 0.1 x 0.5mm. Gd3+, a competitive inhibitor of Mg2+, has a useful anomalous absorption edge at the CuK wavelength and therefore was used in the co-crystallization or soaking conditions. -Mg2+/+Li+/+Ins(1,3,4)P3/+Gd3+ (data=ip7r): Reservoir solution consisted of 10% PEG 8000, 80mM Bis-Tris, pH 5.25, 2mM Gd2(SO4)3, 1mM Ins(1,3,4)P3; 200mM Li2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.64	α = 90
b = 51.64	β = 90
c = 143.33	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	296	AREA DETECTOR	UCSD MARK II		1994-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.542

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	3.2	10.22	85	0.103	3.8	2.1		11374

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.2	3.45			0.193

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	1INP	3.2	10.22	5527	340	94.61	0.20161	0.19883	0.2	0.24551	0.24	RANDOM	34.415

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]
0.76			0.76		-1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.071
r_dihedral_angle_3_deg	12.952
r_dihedral_angle_4_deg	9.438
r_dihedral_angle_1_deg	6.124
r_long_range_B_refined	3.661
r_long_range_B_other	3.388
r_mcangle_it	1.041
r_mcangle_other	1.041
r_angle_refined_deg	1.04
r_angle_other_deg	0.99
r_mcbond_it	0.547
r_mcbond_other	0.547
r_scangle_other	0.471
r_scbond_it	0.221
r_scbond_other	0.198
r_chiral_restr	0.026
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2536
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
UCSD-system	data reduction
UCSD-system	data scaling
SQUASH	phasing