8IAW

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate

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, SITTING DROP	7.5	298	Details about the temperature: 20mM MgCl2, 1mM CoCl2, 35mM Na HEPES-HCl pH7.5, 1M (NH4)2SO4, 0.5mM Spermine, 37.5mM NaCl,500mM KCl, 5mM PEP

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.057	α = 90
b = 110.372	β = 90
c = 130.931	γ = 90

Symmetry
Space Group	P 21 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 EIGER X 16M	Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror.	2022-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.900	SPring-8	BL44XU

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	2.89	50	99.8	0.171	0.18899999999999997	0.995	9.68	5.56		31733

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	2.89	3.07			1.01	1.119	0.8440000000000001

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.89	48.58	30120	1586	99.72	0.24244	0.24082	0.27276	RANDOM	49.756

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]
2.19			4.37		-6.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.997
r_dihedral_angle_3_deg	21.511
r_dihedral_angle_4_deg	19.126
r_long_range_B_refined	10.614
r_long_range_B_other	10.613
r_scangle_other	6.294
r_dihedral_angle_1_deg	6.181
r_mcangle_it	5.45
r_mcangle_other	5.45
r_scbond_it	3.811
r_scbond_other	3.799
r_mcbond_it	3.425
r_mcbond_other	3.424
r_angle_other_deg	2.342
r_angle_refined_deg	1.477
r_chiral_restr	0.059
r_bond_other_d	0.036
r_bond_refined_d	0.007
r_gen_planes_other	0.006
r_gen_planes_refined	0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7680
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	52

Software

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