8IAS

Crystal structure of Streptococcus pneumoniae pyruvate kinase

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	5.5	298	50mM Sodium citrate pH5.5, 11% PEG1000, 10mM Na HEPES pH7.5, 75mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.094	α = 101.22
b = 84.705	β = 96.82
c = 107.012	γ = 91.42

Symmetry
Space Group	P 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 EIGER X 16M	Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror.	2021-11-26	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	49.07	96.7	0.087	0.102	0.997	9.78	3.58		168397

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	2.12			0.785	0.929	0.6920000000000001

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	49.07	159970	8420	96.77	0.17996	0.17809	0.21519	RANDOM	39.222

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]
0.75	-0.34	0.29	1.56	-0.93	-1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.681
r_dihedral_angle_4_deg	21.547
r_dihedral_angle_3_deg	18.494
r_long_range_B_refined	8.77
r_long_range_B_other	8.762
r_scangle_other	7.002
r_scbond_it	4.55
r_scbond_other	4.549
r_dihedral_angle_1_deg	4.427
r_mcangle_it	4.286
r_mcangle_other	4.286
r_mcbond_it	3.18
r_mcbond_other	3.175
r_angle_other_deg	2.304
r_angle_refined_deg	1.465
r_chiral_restr	0.073
r_bond_other_d	0.036
r_bond_refined_d	0.011
r_gen_planes_other	0.008
r_gen_planes_refined	0.006
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	15344
Nucleic Acid Atoms
Solvent Atoms	857
Heterogen Atoms	32

Software

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