3KE3

Crystal structure of Putative serine-pyruvate aminotransferase (YP_263484.1) from PSYCHROBACTER ARCTICUM 273-4 at 2.20 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	25.0000% polyethylene glycol 4000, 0.2000M ammonium sulfate, 0.1M sodium acetate pH 4.6, Additive: 0.001M pyridoxal-5'-phospate (PLP), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.645	α = 90
b = 98.352	β = 90
c = 121.072	γ = 90

Symmetry
Space Group	C 2 2 21

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 mirror, vertical and horizontal focussing mirrors	2009-05-21	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.91162,0.97956,0.97938	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	29.867	99.8	0.125	0.125	8.8	3.7		19035			32.162

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	2.2	2.26	99.9		0.652	0.652	1.2	3.7	1388

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	2.2	29.867	19024	983	99.77	0.169	0.167	0.21	RANDOM	18.099

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]
-1.67			1.8		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.33
r_dihedral_angle_4_deg	17.055
r_dihedral_angle_3_deg	14.128
r_scangle_it	5.506
r_dihedral_angle_1_deg	4.756
r_scbond_it	3.935
r_mcangle_it	2.1
r_angle_refined_deg	1.543
r_angle_other_deg	1.139
r_mcbond_it	1.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.33
r_dihedral_angle_4_deg	17.055
r_dihedral_angle_3_deg	14.128
r_scangle_it	5.506
r_dihedral_angle_1_deg	4.756
r_scbond_it	3.935
r_mcangle_it	2.1
r_angle_refined_deg	1.543
r_angle_other_deg	1.139
r_mcbond_it	1.069
r_mcbond_other	0.204
r_chiral_restr	0.094
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2847
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	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 R01GM157729.