9HA9 | pdb_00009ha9

Central domain fragment of Glucan Water Dikinase-1 from S.tuberosum

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		285	2 M NaCl, 10 % PEG 6K

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.312	α = 90
b = 110.312	β = 90
c = 209.177	γ = 90

Symmetry
Space Group	P 41 21 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 PILATUS 6M		2022-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9793	ALBA	XALOC

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	3	50	100	0.102	3.1	25.9		26669

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	3	3.16			0.742

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3	50	26625	1336	99.985	0.216	0.2146	0.2115	0.2381	0.2334	113.608

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]
2.112			2.112		-4.224

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.032
r_dihedral_angle_6_deg	11.708
r_lrange_it	5.933
r_lrange_other	5.932
r_dihedral_angle_1_deg	5.614
r_dihedral_angle_2_deg	4.808
r_mcangle_it	2.534
r_mcangle_other	2.534
r_scangle_it	2.465
r_scangle_other	2.465
r_mcbond_it	1.481
r_mcbond_other	1.48
r_scbond_it	1.4
r_scbond_other	1.399
r_angle_refined_deg	0.899
r_angle_other_deg	0.34
r_nbd_refined	0.211
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.166
r_xyhbond_nbd_refined	0.148
r_nbd_other	0.139
r_symmetry_nbd_refined	0.137
r_symmetry_nbtor_other	0.07
r_ncsr_local_group_1	0.061
r_chiral_restr	0.044
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7081
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing