Experiment: 8WR2

Crystal Structure of Human Pyridoxal Kinase with bound Luteolin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YXT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291.5	100 mM HEPES pH 7.0, 66% v/v MPD, and 3% w/v D-(+)-Thehalose dihydrate

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.54	α = 90
b = 116.11	β = 90
c = 169.08	γ = 90

Symmetry
Space Group	I 2 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 PILATUS3 6M		2023-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.987	SSRF	BL18U1

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	1.94	47.86	99.95	1	24.45	2		68964

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	1.94	2.009			0.01265	0.01789	0.01265	1	2.09

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2YXT	1.94	47.48	1.35	68958	3436	99.97	0.185	0.1837	0.1856	0.2089	0.2129

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	12.91
f_angle_d	0.962
f_chiral_restr	0.06
f_plane_restr	0.009
f_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4860
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	154

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data reduction
PDB_EXTRACT	data extraction
PHASER	phasing