3P6K

Crystal structure of a PLP-dependent aminotransferase (ZP_03625122.1) from Streptococcus suis 89-1591 at 2.07 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.20M lithium sulfate 2.00M ammonium sulfate, Additive: 0.001M pyridoxal 5'-phosphate (PLP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.979	α = 90
b = 83.979	β = 90
c = 176.391	γ = 120

Symmetry
Space Group	P 32 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 325 mm CCD		2010-07-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97920,0.97903	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.07	29.399	99.1	0.052	15.2			44694		-3	31.925

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.14	98.6		0.514	2

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	MAD	THROUGHOUT	2.07	29.399	44641	2249	99.82	0.1797	0.1782	0.2079	RANDOM	51.4943

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]
0.82	0.41		0.82		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.811
r_dihedral_angle_4_deg	15.923
r_dihedral_angle_3_deg	11.943
r_dihedral_angle_1_deg	4.306
r_scangle_it	3.358
r_scbond_it	2.018
r_angle_refined_deg	1.794
r_angle_other_deg	1.374
r_mcangle_it	1.173
r_mcbond_it	0.624

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.811
r_dihedral_angle_4_deg	15.923
r_dihedral_angle_3_deg	11.943
r_dihedral_angle_1_deg	4.306
r_scangle_it	3.358
r_scbond_it	2.018
r_angle_refined_deg	1.794
r_angle_other_deg	1.374
r_mcangle_it	1.173
r_mcbond_it	0.624
r_mcbond_other	0.184
r_chiral_restr	0.11
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5939
Nucleic Acid Atoms
Solvent Atoms	305
Heterogen Atoms	43

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	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 R01GM133198.