3OP7

Crystal structure of a PLP-dependent aminotransferase (ZP_03625122.1) from Streptococcus suis 89-1591 at 1.70 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.20M lithium sulfate, 2.00M ammonium sulfate, Additive: 0.001M pyridoxal 5'-phosphate (PLP), NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.518	α = 90
b = 97.518	β = 90
c = 89.244	γ = 90

Symmetry
Space Group	P 41 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	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2010-07-23	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.7	29.748	100	0.087	11.2	7.3	47906	47906			24.986

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.74	100		0.92	0.92	0.8	7.3	3505

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	SAD	THROUGHOUT	1.7	29.748	47834	2423	99.96	0.1653	0.1636	0.1974	RANDOM	35.7562

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]
-1.69			-1.69		3.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.671
r_dihedral_angle_4_deg	19.35
r_dihedral_angle_3_deg	13.995
r_dihedral_angle_1_deg	6.155
r_scangle_it	3.651
r_scbond_it	2.344
r_angle_refined_deg	1.671
r_mcangle_it	1.38
r_angle_other_deg	0.984
r_mcbond_it	0.831

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.671
r_dihedral_angle_4_deg	19.35
r_dihedral_angle_3_deg	13.995
r_dihedral_angle_1_deg	6.155
r_scangle_it	3.651
r_scbond_it	2.344
r_angle_refined_deg	1.671
r_mcangle_it	1.38
r_angle_other_deg	0.984
r_mcbond_it	0.831
r_mcbond_other	0.272
r_chiral_restr	0.099
r_bond_refined_d	0.017
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2967
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	51

Software

Software
Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

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.