8XW9

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and UDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8XW6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	10mM HEPES pH7.5, 75mM NaCl, 125mM KCl, 10mM Tris-HCl pH7.0, 14% PEG4000, 10mM Oxalate, 10mM FBP, 5mM UDP

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.464	α = 90
b = 81.464	β = 90
c = 398.91	γ = 90

Symmetry
Space Group	P 43 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		2023-12-04	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	1.75	40.74	99.5	0.057	0.063	0.9990000000000001	16.01	6		136776

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	1.75	1.85			0.9359999999999999	1.024	0.672

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	1.75	40.73	129937	6839	99.48	0.16174	0.16023	0.19057	RANDOM	34.335

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]
0.43			0.43		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.178
r_dihedral_angle_4_deg	16.123
r_dihedral_angle_3_deg	14.53
r_long_range_B_refined	8.55
r_long_range_B_other	8.55
r_scangle_other	7.561
r_dihedral_angle_1_deg	6.286
r_scbond_other	4.987
r_scbond_it	4.986
r_mcangle_other	3.835
r_mcangle_it	3.832
r_mcbond_it	2.95
r_mcbond_other	2.942
r_angle_other_deg	2.351
r_angle_refined_deg	1.783
r_chiral_restr	0.091
r_bond_other_d	0.036
r_gen_planes_other	0.017
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
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	911
Heterogen Atoms	82

Software

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