7TN8 | pdb_00007tn8

Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1 mutant (ZmITPK1-H192A) in complex with InsP6

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	12% PEG3350, 100 mM HEPES, 7.0, 200 mM calcium chloride, 10% glycerol

Crystal Properties
Matthews coefficient	Solvent content
4.09	69.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.07	α = 90
b = 99.07	β = 90
c = 215.444	γ = 120

Symmetry
Space Group	P 61 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	PIXEL	DECTRIS EIGER X 16M		2020-12-03	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 Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.6	50	99.7	0.066	0.07	0.023	15.5	9.9		20094

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	99.8		0.849	0.891	0.269	0.881		10.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.6	42.11	18995	996	99.3	0.2047	0.2021	0.21	0.2517	0.25	RANDOM	43.691

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]
-0.24	-0.12		-0.24		0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.214
r_dihedral_angle_3_deg	18.77
r_dihedral_angle_4_deg	15.643
r_dihedral_angle_1_deg	8.956
r_angle_refined_deg	1.928
r_angle_other_deg	1.278
r_chiral_restr	0.103
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.214
r_dihedral_angle_3_deg	18.77
r_dihedral_angle_4_deg	15.643
r_dihedral_angle_1_deg	8.956
r_angle_refined_deg	1.928
r_angle_other_deg	1.278
r_chiral_restr	0.103
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2184
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.