3DXP | pdb_00003dxp

Crystal structure of a putative aminoglycoside phosphotransferase (reut_a1007) from ralstonia eutropha jmp134 at 2.32 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.17	293	20.0% polyethylene glycol 8000, 0.3M calcium acetate, 0.1M MES pH 6.17, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.088	α = 90
b = 127.522	β = 90
c = 51.509	γ = 90

Symmetry
Space Group	P 21 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	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-06-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97971,0.97956	SSRL	BL9-2

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	2.32	28.989	99.9	0.129	0.129	5.3	3.5		18395			33.49

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)
	2.32	2.38	100		0.718	0.718	1.1	3.5	1329

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	2.32	28.989	17366	898	94.49	0.238	0.235	0.24	0.287	0.29	RANDOM	37.949

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]
-3.58			-3.53		7.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.02
r_dihedral_angle_3_deg	12.922
r_dihedral_angle_4_deg	12.686
r_scangle_it	5.791
r_scbond_it	4.271
r_dihedral_angle_1_deg	2.946
r_mcangle_it	2.776
r_mcbond_it	1.72
r_angle_refined_deg	1.479
r_angle_other_deg	0.939
r_mcbond_other	0.277
r_nbd_refined	0.201
r_nbd_other	0.193
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.169
r_symmetry_vdw_other	0.166
r_metal_ion_refined	0.165
r_symmetry_vdw_refined	0.128
r_chiral_restr	0.091
r_nbtor_other	0.087
r_symmetry_hbond_refined	0.039
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2563
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	9

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing