2BKK | pdb_00002bkk

Crystal structure of Aminoglycoside Phosphotransferase APH(3')-IIIa in complex with the inhibitor AR_3a

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MJO	PDB ENTRIES 1MJO, 1J7L
experimental model	PDB	1J7L	PDB ENTRIES 1MJO, 1J7L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				15-20 % PEG 5500, 0.1 M MES PH 5.9-6.2

Crystal Properties
Matthews coefficient	Solvent content
2.1	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.67	α = 90
b = 98.082	β = 110.01
c = 81.3	γ = 90

Symmetry
Space Group	P 1 21 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	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.15	20	97.2	0.05		3.5		46440		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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1MJO, 1J7L	2.15	20	45310	1122	96.7	0.2	0.199	0.21	0.26	RANDOM	52.8

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]
0.82		2.37	-0.53		1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.877
r_scangle_it	5.907
r_mcangle_it	5.669
r_scbond_it	3.901
r_mcbond_it	3.746
r_angle_refined_deg	1.554
r_angle_other_deg	0.872
r_xyhbond_nbd_refined	0.277
r_symmetry_hbond_refined	0.25
r_nbd_other	0.237
r_nbd_refined	0.23
r_symmetry_vdw_other	0.222
r_symmetry_vdw_refined	0.169
r_chiral_restr	0.096
r_nbtor_other	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6595
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing