2ODT | pdb_00002odt

Structure of human Inositol 1,3,4-trisphosphate 5/6-kinase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	293	1.6 M Citrate, Tris buffer, 0.1 M, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.33	α = 90
b = 39.55	β = 98.4
c = 67.39	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210	Monochromator	2006-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.93	ESRF	ID14-1

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	40	95.5	7.6	11	3.4	21978	20997		-3	15

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)
	2	2.1	77.2		28.9	3.4	2.7	2285

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	2.01	20.22	-3	20616	19922	1064	96.63	0.18117	0.18117	0.17701	0.18	0.25723	0.26	RANDOM	26.824

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]
-0.02			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.626
r_dihedral_angle_4_deg	20.605
r_dihedral_angle_3_deg	16.343
r_dihedral_angle_1_deg	7.456
r_scangle_it	4.431
r_scbond_it	3.02
r_mcangle_it	1.879
r_angle_refined_deg	1.802
r_mcbond_it	1.148
r_nbtor_refined	0.316
r_symmetry_hbond_refined	0.288
r_nbd_refined	0.244
r_xyhbond_nbd_refined	0.217
r_symmetry_vdw_refined	0.19
r_chiral_restr	0.12
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
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_refined
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2541
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	data collection
XDS	data reduction
XSCALE	data scaling
SHARP	phasing