4O4B

Crystal Structure of an Inositol hexakisphosphate kinase EhIP6KA as a fusion protein with maltose binding protein

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EZ9	PDB ENTRIES 1EZ9 AND 1W2C
experimental model	PDB	1W2C	PDB ENTRIES 1EZ9 AND 1W2C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	12% (w/v) PEG 3350, 50 mM NaH2PO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.626	α = 90
b = 51.98	β = 90
c = 117.328	γ = 90

Symmetry
Space Group	P 21 21 21

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 225 mm CCD		2013-02-05	M	SINGLE WAVELENGTH

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

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	1.8	50	99.4	0.057	39.6	5	67725	67725	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	1.8	1.83	99.4		0.457	3.1	4.8	3301

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1EZ9 AND 1W2C	1.8	36.97	64104	64104	3383	98.66	0.19744	0.19744	0.19618	0.22102	RANDOM	35.793

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]
-0.23			-0.19		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.361
r_dihedral_angle_4_deg	13.413
r_dihedral_angle_3_deg	13.181
r_long_range_B_refined	9.271
r_long_range_B_other	9.156
r_dihedral_angle_1_deg	5.444
r_mcangle_it	1.486
r_mcangle_other	1.486
r_scangle_other	1.42
r_angle_refined_deg	1.1
r_scbond_it	0.844
r_scbond_other	0.844
r_mcbond_it	0.835
r_mcbond_other	0.835
r_angle_other_deg	0.74
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_bond_other_d	0.005
r_gen_planes_refined	0.004
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	4982
Nucleic Acid Atoms
Solvent Atoms	654
Heterogen Atoms

Software

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