2QIR | pdb_00002qir

Crystal structure of aminoglycoside acetyltransferase AAC(6')-Ib in complex whith coenzyme A and kanamycin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PRB	pdb entry 2prb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	K2HPO4 1.5 M, NaH2PO4 0.06M, Guanidine 0.1M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.404	α = 90
b = 57.404	β = 90
c = 145.57	γ = 90

Symmetry
Space Group	P 43 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	77	CCD	ADSC QUANTUM 210		2007-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	2.4	53.402	100	0.081	0.081	8.3	13.4	10187	10187		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	2.4	2.53	100		0.212	0.212	3.4	11.5	1427

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2prb	2.4	45.08	3	10187	10125	490	99.98	0.192	0.194	0.192	0.19	0.235	0.24	RANDOM	15.601

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]
-0.01			-0.01		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.254
r_dihedral_angle_4_deg	14.672
r_dihedral_angle_3_deg	14.086
r_dihedral_angle_1_deg	6.411
r_scangle_it	2.842
r_scbond_it	1.704
r_angle_refined_deg	1.349
r_mcangle_it	1.202
r_mcbond_it	0.75
r_symmetry_hbond_refined	0.385

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.254
r_dihedral_angle_4_deg	14.672
r_dihedral_angle_3_deg	14.086
r_dihedral_angle_1_deg	6.411
r_scangle_it	2.842
r_scbond_it	1.704
r_angle_refined_deg	1.349
r_mcangle_it	1.202
r_mcbond_it	0.75
r_symmetry_hbond_refined	0.385
r_nbtor_refined	0.3
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.161
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1356
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	81

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
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 R01GM157729.