3K9U | pdb_00003k9u

Crystal structure of paia acetyltransferase (ta0374) from thermoplasma acidophilum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F0A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	0.2 M Sodium Bromide, 20% PEG 3350, 0.1 M Bis-Tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.28	α = 90
b = 70.577	β = 90
c = 87.671	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		MIRROR	2009-03-16	M	MOLECULAR REPLACEMENT

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97872	APS	21-ID-G

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	2.3	54.98	98.7	0.086	0.086	17.469	7	19708	19708		-3

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	2.3	2.34	98.6		0.185	0.185	10.2	6.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	3F0A	2.3	54.98	19697	19697	1001	98.57	0.194	0.191	0.2	0.247	0.25	RANDOM	21.28

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]
-0.73			1.25		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.362
r_dihedral_angle_4_deg	22.885
r_dihedral_angle_3_deg	16.802
r_dihedral_angle_1_deg	6.076
r_scangle_it	4.551
r_scbond_it	2.855
r_mcangle_it	1.746
r_angle_refined_deg	1.472
r_mcbond_it	0.901
r_angle_other_deg	0.858

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.362
r_dihedral_angle_4_deg	22.885
r_dihedral_angle_3_deg	16.802
r_dihedral_angle_1_deg	6.076
r_scangle_it	4.551
r_scbond_it	2.855
r_mcangle_it	1.746
r_angle_refined_deg	1.472
r_mcbond_it	0.901
r_angle_other_deg	0.858
r_mcbond_other	0.235
r_chiral_restr	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2652
Nucleic Acid Atoms
Solvent Atoms	75
Heterogen Atoms	107

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-3000	data scaling

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.