7K0A | pdb_00007k0a

Puromycin N-acetyltransferase in complex with acetylated puromycin and CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7K09

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.26	281	9.9% (w/v) 1,6-hexanediol, 1.59 M ammonium sulfate, 7.4 % (v/v) polyethylene glycol 400, 0.1 M HEPES pH 8.26, 0.5 n-hexyl-b-D-glucopyranoside

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.596	α = 90
b = 141.509	β = 100.341
c = 98.985	γ = 90

Symmetry
Space Group	I 1 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	ADSC QUANTUM 315r		2016-03-11	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r		2016-03-11	M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	ADSC QUANTUM 315r		2016-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2
2	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2
3	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	70.75	99.9	0.376	0.4	0.136	0.989	7.7	17.2		33396

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	99.4		0.608	0.857	2.3	15.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7K09	2	42.488	33371	1619	99.97	0.209	0.2071	0.22	0.2405	0.25	16.23

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]
-1.713		0.798	-2.055		3.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.425
r_dihedral_angle_4_deg	15.643
r_dihedral_angle_3_deg	13.779
r_dihedral_angle_1_deg	6.514
r_lrange_it	6.204
r_lrange_other	6.109
r_scangle_it	3.355
r_scangle_other	3.234
r_scbond_it	2.201
r_scbond_other	2.092
r_mcangle_it	2.023
r_mcangle_other	2.023
r_angle_refined_deg	1.621
r_angle_other_deg	1.331
r_mcbond_it	1.268
r_mcbond_other	1.263
r_nbd_refined	0.213
r_nbd_other	0.196
r_xyhbond_nbd_refined	0.192
r_symmetry_nbd_other	0.183
r_symmetry_xyhbond_nbd_refined	0.182
r_symmetry_nbd_refined	0.163
r_nbtor_refined	0.162
r_symmetry_xyhbond_nbd_other	0.13
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.082
r_ncsr_local_group_1	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2968
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	226

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing