3HAM | pdb_00003ham

Structure of the gentamicin-APH(2")-IIa complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	unbuffered 16% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.7	α = 90
b = 58.8	β = 98.4
c = 81.4	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	ADSC QUANTUM 315		2004-06-29	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	2.5	80.6	98.9	0.042	21.4			25799		2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.5	35	24499	1299	98.93	0.21319	0.21002	0.2	0.27103	0.26	RANDOM	38.614

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]
2.55		0.29	-3.12		0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.529
r_dihedral_angle_3_deg	19.266
r_dihedral_angle_4_deg	17.919
r_dihedral_angle_1_deg	5.694
r_scangle_it	2.517
r_scbond_it	1.656
r_angle_refined_deg	1.301
r_mcangle_it	1.024
r_mcbond_it	0.602
r_nbtor_refined	0.32
r_nbd_refined	0.235
r_symmetry_hbond_refined	0.211
r_xyhbond_nbd_refined	0.191
r_symmetry_vdw_refined	0.191
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4978
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	86

Software

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