8G1Y | pdb_00008g1y

Crystal Structure of the Threonine Synthase from Streptococcus pneumoniae in complex with Pyridoxal 5-phosphate.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	292	Protein: 8.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 2mM PLP; Screen: Classics II (B11), 2.1M DL-Malic acid pH 7.0; Cryo: 25% glycerol in screen solution.

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.464	α = 90
b = 81.413	β = 94.6
c = 139.465	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	MARMOSAIC 300 mm CCD	Be	2021-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9787	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	1.43	30	94.4	0.078	0.078	0.087	0.039	0.995	19.5	4.8		167626		-3	13.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.43	1.45	90.6		0.853	0.853	0.96	0.434	0.792	1.9	4.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.43	29.29	159092	8365	94.3	0.1578	0.1568	0.16	0.1769	0.18	RANDOM	16.724

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]
-0.33		0.02	-0.47		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.343
r_dihedral_angle_4_deg	18.413
r_dihedral_angle_3_deg	9.198
r_dihedral_angle_1_deg	4.095
r_angle_refined_deg	1.381
r_angle_other_deg	0.373
r_chiral_restr	0.069
r_gen_planes_refined	0.056
r_gen_planes_other	0.051
r_bond_refined_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.343
r_dihedral_angle_4_deg	18.413
r_dihedral_angle_3_deg	9.198
r_dihedral_angle_1_deg	4.095
r_angle_refined_deg	1.381
r_angle_other_deg	0.373
r_chiral_restr	0.069
r_gen_planes_refined	0.056
r_gen_planes_other	0.051
r_bond_refined_d	0.005
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7592
Nucleic Acid Atoms
Solvent Atoms	1113
Heterogen Atoms	99

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.