3CSV | pdb_00003csv

Crystal structure of a putative aminoglycoside phosphotransferase (YP_614837.1) from Silicibacter sp. TM1040 at 2.15 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	NANODROP, 2.0M (NH4)2SO4, 0.2M NaCl, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.68	α = 90
b = 55.94	β = 102.9
c = 61.22	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97915	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	2.15	29.735	98.2	0.055	10.33			20496		-3	29.356

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.23	96.5		0.322	2.4

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	SAD	THROUGHOUT	2.15	29.735	20494	1050	99.64	0.171	0.168	0.17	0.228	0.23	RANDOM	26.368

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]
-0.56		-0.19	1.11		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.156
r_dihedral_angle_4_deg	14.064
r_dihedral_angle_3_deg	13.222
r_scangle_it	6.405
r_dihedral_angle_1_deg	5.588
r_scbond_it	4.455
r_mcangle_it	2.425
r_mcbond_it	1.35
r_angle_refined_deg	1.174
r_angle_other_deg	0.906
r_mcbond_other	0.321
r_symmetry_vdw_other	0.258
r_nbd_refined	0.206
r_nbd_other	0.196
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.157
r_symmetry_vdw_refined	0.157
r_symmetry_hbond_refined	0.152
r_nbtor_other	0.084
r_chiral_restr	0.07
r_metal_ion_refined	0.011
r_bond_refined_d	0.01
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	2531
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	52

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing