9QVI | pdb_00009qvi

Central domain of Glucan Water Dikinase-1 in alternative closed conformation

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9HA9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		285	0.1 M HEPES Na salt pH 7.5, 0.7 M tri-Na citrate

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.134	α = 90
b = 94.134	β = 90
c = 150.757	γ = 90

Symmetry
Space Group	P 43 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		2022-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	3.25	49.89	100	0.046	0.999	5	12.7		11258

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.25	3.43			0.749	0.966	1

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	3.25	47.111	11212	531	99.875	0.301	0.2995	0.2937	0.3279	0.3217	198.156

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]
1.711			1.711		-3.423

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.083
r_lrange_it	13.149
r_lrange_other	13.149
r_dihedral_angle_6_deg	11.169
r_mcangle_it	6.005
r_mcangle_other	6.004
r_scangle_it	5.843
r_scangle_other	5.842
r_dihedral_angle_1_deg	5.652
r_dihedral_angle_2_deg	5.504
r_mcbond_it	3.595
r_mcbond_other	3.595
r_scbond_it	3.399
r_scbond_other	3.398
r_angle_refined_deg	0.992
r_angle_other_deg	0.392
r_symmetry_nbd_refined	0.343
r_nbd_refined	0.265
r_nbd_other	0.237
r_symmetry_nbd_other	0.197
r_xyhbond_nbd_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.186
r_xyhbond_nbd_other	0.079
r_symmetry_xyhbond_nbd_other	0.074
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.05
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	3487
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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