6FUX | pdb_00006fux

Structure of aminoglycoside phosphotransferase APH(3'')-Id from Streptomyces rimosus ATCC10970 in complex with ADP and streptomycin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6FUC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	277	0.1M MES monohydrate; 12% PEG20000

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.97	α = 90
b = 77.8	β = 90
c = 78.61	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	PIXEL	DECTRIS PILATUS3 6M		2016-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.65	55.3	98.8	0.138	0.151	0.992	8.04	5.952		34969			27.329

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.7	98.2		0.651	0.71	0.825	2.2	6.197

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 (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	6FUC	1.65	55.3	33229	1740	98.8	0.1699	0.1683	0.18	0.2021	0.22	RANDOM	28.84

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]
-0.52			-2.17		2.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.543
r_dihedral_angle_4_deg	23.303
r_dihedral_angle_3_deg	15.265
r_dihedral_angle_1_deg	6.826
r_angle_refined_deg	2.76
r_angle_other_deg	2.519
r_chiral_restr	0.416
r_bond_refined_d	0.021
r_gen_planes_refined	0.016
r_gen_planes_other	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.543
r_dihedral_angle_4_deg	23.303
r_dihedral_angle_3_deg	15.265
r_dihedral_angle_1_deg	6.826
r_angle_refined_deg	2.76
r_angle_other_deg	2.519
r_chiral_restr	0.416
r_bond_refined_d	0.021
r_gen_planes_refined	0.016
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2059
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

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.