4JXQ | pdb_00004jxq

Crystal structure of a GNAT superfamily phosphinothricin acetyltransferase (Pat) from Sinorhizobium meliloti 1021

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	289	0.2 M di-Ammonium citrate pH 5.0, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.461	α = 90
b = 80.481	β = 90
c = 83.611	γ = 90

Symmetry
Space Group	P 21 21 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	ADSC QUANTUM 315r	mirrors	2013-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

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	1.15	32.47	98	0.068	0.068	46.9	7.7	121117	121117		-3	11.6

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	1.15	1.17	82.3		0.628	0.628	2	3.9	5028

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.15	32.47	114953	114953	6058	97.85	0.12173	0.12173	0.12008	0.12	0.15257	0.15	RANDOM	17.885

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]
0.6			-0.49		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.585
r_sphericity_free	31.075
r_dihedral_angle_4_deg	16.674
r_sphericity_bonded	14.319
r_dihedral_angle_3_deg	12.568
r_rigid_bond_restr	8.034
r_dihedral_angle_1_deg	6.129
r_angle_refined_deg	1.983
r_angle_other_deg	1.099
r_chiral_restr	0.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.585
r_sphericity_free	31.075
r_dihedral_angle_4_deg	16.674
r_sphericity_bonded	14.319
r_dihedral_angle_3_deg	12.568
r_rigid_bond_restr	8.034
r_dihedral_angle_1_deg	6.129
r_angle_refined_deg	1.983
r_angle_other_deg	1.099
r_chiral_restr	0.111
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2833
Nucleic Acid Atoms
Solvent Atoms	669
Heterogen Atoms	65

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
DM	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.