6WRR | pdb_00006wrr

CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AND LITHIUM AT 2.5 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	6.3	293	13% PEG8000, 200mM Li2SO4 and 100mM Tris, pH 6.3. Upon reaching maximum size after ~5 days, a Gd3+ heavy atom derivative was prepared by adding 0.5uL of 17.5mM Gd2(SO4)3 in reservoir solution to 3uL hanging drops (2.5mM final Gd3+) containing native crystals for 48 hours

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		1992-07-10	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	2.5	15.45	96	0.051	10.8	3.4		26197

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	2.5	2.69	95.6		0.172

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	2.5	15.45	11645	725	99.98	0.16537	0.16286	0.2	0.20497	0.24	RANDOM	32.228

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]
0.78			0.78		-1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.225
r_dihedral_angle_3_deg	15.766
r_dihedral_angle_4_deg	13.114
r_dihedral_angle_1_deg	5.254
r_scangle_it	1.333
r_angle_refined_deg	1.056
r_scbond_it	0.819
r_mcangle_it	0.748
r_mcbond_it	0.432
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.211
r_nbd_refined	0.181
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.069
r_metal_ion_refined	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2532
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	12

Software

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