4O4F | pdb_00004o4f

Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA in complexed with ATP and InsP6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O4C	PDB Entry 4O4C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	277	0.4 M NaH2PO4 in the presence of 10 mM ATP,5 mM IP3, 20 mM MgCl2. The crystals were further soaked under 22% (w/v) PEG 3350, 10 mM MgCl2, 10 mM ATP, 0.1 M sodium acetate, pH 5.2, 20 mM IP6 for 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.229	α = 90
b = 102.229	β = 90
c = 109.493	γ = 90

Symmetry
Space Group	I 41 2 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	CCD	MARMOSAIC 300 mm CCD		2013-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	1.7	50	96.4	0.053	56.7	9.8	31175	31175	3

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	1.7	1.73	71.6		0.54	2.4	5.2	1145

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB Entry 4O4C	1.7	34.4	29589	29589	1568	96.13	0.19277	0.19277	0.19129	0.2	0.2218	0.23	RANDOM	32.582

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]
-0.92			-0.92		1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.396
r_dihedral_angle_4_deg	14.141
r_dihedral_angle_3_deg	13.525
r_long_range_B_refined	6.672
r_long_range_B_other	6.511
r_dihedral_angle_1_deg	6.494
r_scangle_other	3.077
r_mcangle_it	2.571
r_mcangle_other	2.57
r_scbond_it	1.881
r_scbond_other	1.876
r_angle_refined_deg	1.825
r_mcbond_other	1.564
r_mcbond_it	1.563
r_angle_other_deg	1.016
r_chiral_restr	0.399
r_bond_refined_d	0.01
r_bond_other_d	0.006
r_gen_planes_refined	0.006
r_gen_planes_other	0.001
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	2046
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	79

Software

Software
Software Name	Purpose
HKL-2000	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing