9QV4 | pdb_00009qv4

1-Phosphofructokinase mutant K95T/G110S from E. coli with bound fructose-1,6-bisphosphate and ADP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	The FruK variant K95T/G110S (3.5 mg/mL) in 20 mM MOPS/KOH buffer (pH 7.4) containing 75 mM KCl and 1 M L-proline was mixed in a 1:1 ratio with condition containing 26 % (w/v) pentaerythritol ethoxylate, 75 mM MES (pH 6.5), 150 mM ammonium sulfate, 8 mM fructose-6-phosphate, 4 mM ADP, and 10 mM magnesium chloride. The final drop volume was 0.8 microliters. Before plunge freezing in liquid nitrogen, the crystals were soaked with addintional 20 mM fructose-6-phosphate, 2 mM ADP, 5 mM magnesium chloride for about 1 minute, before glycerol was added as a cryo-protectant to a final concentration of 30% (v/v).

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.12	α = 90
b = 98.21	β = 90
c = 140.1	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 EIGER X 16M		2020-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.97625	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.55	19.74	99.6	0.055	0.058	1	25.55	13.4		63211

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.59			0.831	0.872	0.833

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	1.55	19.74	1.36	63195	1998	99.67	0.1603	0.1598	0.16	0.1742	0.1746

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	14.784
f_angle_d	1.012
f_chiral_restr	0.055
f_plane_restr	0.009
f_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2339
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	56

Software

Software
Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHENIX	phasing
PDB_EXTRACT	data extraction