2XAO | pdb_00002xao

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with IP5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XAM	PDB ENTRY 2XAM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.9		22% PEG 3300, 100 MM BIS-TRIS PH 5.9, 2 MM MGCL2. PROTEIN WAS MIXED WITH 2 MM INOSITOL-5-P

Crystal Properties
Matthews coefficient	Solvent content
2.3	47.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.761	α = 90
b = 112.737	β = 90
c = 144.454	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	120	CCD	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.7	88.74	100	0.13	4.24	6.92		22033		2	57

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.06	100		0.45	1.66	6.99

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2XAM	2.9	88.736	21980	1141	99.995	0.228	0.2249	0.22	0.2907	0.28	RANDOM	38.993

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]
0.267			-1.716		1.449

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.168
r_dihedral_angle_3_deg	20.117
r_dihedral_angle_4_deg	19.598
r_dihedral_angle_1_deg	5.543
r_scangle_it	1.847
r_angle_refined_deg	1.371
r_scbond_it	1.067
r_mcangle_it	0.937
r_mcbond_it	0.524
r_nbtor_refined	0.306
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.215
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.09
r_symmetry_hbond_refined	0.086
r_metal_ion_refined	0.063
r_bond_refined_d	0.01
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	6602
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling