6P63

Wild-type NIS synthetase DesD bound to AMP and substrate analog cadaverine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	0.16 M magnesium chloride, 20% PEG, 0.08 M Tris hexahydrate, pH 8.5, 15% glycerol, 10% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.43	α = 90
b = 74.24	β = 94.7
c = 183.17	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	80	IMAGE PLATE	RIGAKU RAXIS HTC	varimax DW	2014-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU R-AXIS IV	1.54180

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.4	89.53	96.2	0.09	0.121	0.081	0.993	9.5	3.8		99262

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	94.3		0.344	0.456	0.296	0.841	3.5	3.9

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2X0O	2.4	69.832	99234	4971	95.851	0.171	0.1681	0.2267	RANDOM	22.251

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]
0.763		-0.357	-0.661		-0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.525
r_dihedral_angle_4_deg	21.252
r_dihedral_angle_3_deg	16.28
r_dihedral_angle_1_deg	8.096
r_lrange_it	3.419
r_lrange_other	3.419
r_angle_other_deg	2.405
r_angle_refined_deg	1.846
r_mcangle_it	1.471
r_mcangle_other	1.471
r_scangle_it	1.388
r_scangle_other	1.388
r_mcbond_it	0.818
r_mcbond_other	0.818
r_scbond_it	0.813
r_scbond_other	0.813
r_symmetry_nbd_other	0.22
r_nbd_refined	0.21
r_nbd_other	0.21
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.16
r_symmetry_nbd_refined	0.156
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_other	0.056
r_bond_other_d	0.035
r_metal_ion_refined	0.03
r_gen_planes_other	0.013
r_bond_refined_d	0.012
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18780
Nucleic Acid Atoms
Solvent Atoms	937
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CrystalClear	data scaling
PHASER	phasing