44XA | pdb_000044xa

Crystal structure of the pyrophosphate-dependent phosphofructokinase from Promethearchaeum syntrophicum with fructose 6-phosphate

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, HANGING DROP	9	291	1 M MMT pH 9.0, 20 - 30 % PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.21	α = 90
b = 71.866	β = 91.079
c = 136.53	γ = 90

Symmetry
Space Group	P 1 21 1

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 EIGER2 S 16M		2022-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95366	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim 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	2.5	45.5	100	0.148	0.053	0.996	9	7.6		51164

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.68			1.587	0.561	0.719	1.9

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	2.6	45.5	51113	2601	99.894	0.25	0.24172	0.2462	0.27963	0.29	49.531

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]
-4.134		2.023	2.836		1.222

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.53
r_dihedral_angle_3_deg	15.789
r_dihedral_angle_2_deg	12.891
r_lrange_it	6.902
r_lrange_other	6.902
r_scangle_it	6.179
r_scangle_other	6.178
r_mcangle_it	5.566
r_mcangle_other	5.566
r_dihedral_angle_1_deg	5.343
r_scbond_it	4.834
r_scbond_other	4.828
r_mcbond_it	4.029
r_mcbond_other	4.027
r_angle_refined_deg	1.582
r_angle_other_deg	0.836
r_symmetry_nbd_other	0.237
r_nbd_other	0.231
r_nbd_refined	0.225
r_nbtor_refined	0.189
r_symmetry_nbd_refined	0.167
r_ncsr_local_group_3	0.167
r_ncsr_local_group_5	0.166
r_ncsr_local_group_2	0.165
r_ncsr_local_group_4	0.161
r_ncsr_local_group_6	0.156
r_ncsr_local_group_1	0.155
r_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.072
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10789
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing