7TN3 | pdb_00007tn3

Crystal structure of Zea mays Inositol-tetrakisphosphate Kinase 1 mutant (ZmITPK1-F189A/H192A)

X-RAY DIFFRACTION

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.594	α = 90
b = 98.594	β = 90
c = 202.571	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		2020-12-12	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	2.9	50	99.9	0.097	0.099	0.021	10.7	23.8		13583

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	2.9	2.95	100		0.965	0.985	0.193	0.963		25.6

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	2.9	49.35	12186	654	94.73	0.2316	0.229	0.24	0.2803	0.29	RANDOM	50.937

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]
-0.13	-0.07		-0.13		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.455
r_dihedral_angle_3_deg	20.64
r_dihedral_angle_4_deg	19.955
r_dihedral_angle_1_deg	9.187
r_angle_refined_deg	1.966
r_angle_other_deg	1.232
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.455
r_dihedral_angle_3_deg	20.64
r_dihedral_angle_4_deg	19.955
r_dihedral_angle_1_deg	9.187
r_angle_refined_deg	1.966
r_angle_other_deg	1.232
r_chiral_restr	0.084
r_bond_refined_d	0.012
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	2081
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
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.