9U3W | pdb_00009u3w

Crystal structure of the ribokinase RBK1 in complex with ribose from Saccharomyces cerevisiae

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		291	0.2M Sodium formate, 0.1M Bicine pH 8.6, 24% PEG 5000, 0.04% 1,2-Diaminocyclohexane sulfate, 0.04% Diloxanide furoate, 0.04% Fumaric acid, 0.04% Spermine, 0.04% Sulfaguanidine, 0.004M HEPES sodium pH 6.8

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.84	α = 90
b = 169.06	β = 90
c = 117.87	γ = 90

Symmetry
Space Group	C 2 2 21

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		2023-09-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.978797	SSRF	BL10U2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.91	84.53	99.2	0.997	14.3	12.3		17881

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.91	2.99			0.557

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.91	36.47	1.34	17881	890	98.8	0.2426	0.2402	0.2413	0.2935	0.2947

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.771
f_angle_d	0.864
f_chiral_restr	0.051
f_plane_restr	0.009
f_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4649
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	20

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing