4U13

Crystal structure of putative polyketide cyclase (protein SMa1630) from Sinorhizobium meliloti at 2.3 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 ul of 18 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG condition #96 (0.2 M Lithium Sulfate, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.764	α = 90
b = 42.295	β = 111.83
c = 62.287	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	MARMOSAIC 300 mm CCD	Beryllium Lenses	2013-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.3	50	99.3	0.07	0.07	12.9	3.7		10379		-3	55

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	2.3	2.34	92.5		0.674	2.1	3.2	480

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3fh1	2.3	50	10348	535	98.85	0.1942	0.1926	0.2238	RANDOM	65.057

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]
2.65		1.2	-1.72		-1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.953
r_dihedral_angle_4_deg	17.038
r_dihedral_angle_3_deg	16.349
r_dihedral_angle_1_deg	6.046
r_mcangle_it	4.021
r_mcbond_it	2.652
r_mcbond_other	2.648
r_angle_refined_deg	1.689
r_angle_other_deg	0.992
r_chiral_restr	0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.953
r_dihedral_angle_4_deg	17.038
r_dihedral_angle_3_deg	16.349
r_dihedral_angle_1_deg	6.046
r_mcangle_it	4.021
r_mcbond_it	2.652
r_mcbond_other	2.648
r_angle_refined_deg	1.689
r_angle_other_deg	0.992
r_chiral_restr	0.098
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1635
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data scaling
PHENIX	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.