3HAV | pdb_00003hav

Structure of the streptomycin-ATP-APH(2")-IIa ternary complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HAM	PDB ENTRY 3ham

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.3	277	30% mPEG5000, 0.2 M MOPS/KOH pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.62	α = 90
b = 128.62	β = 90
c = 57.87	γ = 120

Symmetry
Space Group	P 31

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 315		2005-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	SSRL	BL9-2

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	2.45	42.9	99.1	0.043	20.1			41774		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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	PDB ENTRY 3ham	2.45	19.78	37057	1943	99.26	0.22075	0.21756	0.228	0.28382	0.2855	RANDOM	41.756

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]
1.91	0.96		1.91		-2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.858
r_dihedral_angle_3_deg	20.733
r_dihedral_angle_4_deg	19.106
r_dihedral_angle_1_deg	8.008
r_scangle_it	2.009
r_scbond_it	1.333
r_angle_refined_deg	1.192
r_mcangle_it	0.806
r_mcbond_it	0.465
r_nbtor_refined	0.312
r_metal_ion_refined	0.253
r_nbd_refined	0.233
r_symmetry_vdw_refined	0.205
r_symmetry_hbond_refined	0.184
r_xyhbond_nbd_refined	0.178
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7284
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	216

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling