5BP9 | pdb_00005bp9

Crystal structure of SAM-dependent methyltransferase from Bacteroides fragilis in complex with S-Adenosyl-L-homocysteine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	0.2 ul of 15 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 TOP96 condition #29 (0.2 M Ammonium sulfate, 0.1 M Sodium Cacodylate:HCl pH 6.5, 30% (w/v) PEG 8000) 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 1 mg/ml TEV solution at 289 K for 3 hours

Crystal Properties
Matthews coefficient	Solvent content
1.95	31.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.732	α = 90
b = 70.66	β = 90
c = 78.743	γ = 90

Symmetry
Space Group	P 21 21 21

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	2015-04-16	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)	Rrim I (All)	Rpim I (All)	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	1.5	50	98.9	0.062	0.062	0.069	0.03	11.3	5	38281	37846		-3	18.8

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	1.5	1.53	98		0.692	0.784	0.362	0.677	1.9	4.4	1807

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	1.5	50	35821	1836	98.93	0.1341	0.1318	0.1313	0.1795	0.1787	RANDOM	22.973

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]
0.13			0.4		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.027
r_sphericity_bonded	16.133
r_dihedral_angle_4_deg	11.605
r_dihedral_angle_3_deg	11.552
r_rigid_bond_restr	7.225
r_dihedral_angle_1_deg	5.562
r_mcangle_it	3.277
r_mcbond_it	3.105
r_mcbond_other	3.053
r_angle_refined_deg	1.562

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.027
r_sphericity_bonded	16.133
r_dihedral_angle_4_deg	11.605
r_dihedral_angle_3_deg	11.552
r_rigid_bond_restr	7.225
r_dihedral_angle_1_deg	5.562
r_mcangle_it	3.277
r_mcbond_it	3.105
r_mcbond_other	3.053
r_angle_refined_deg	1.562
r_angle_other_deg	1.085
r_chiral_restr	0.093
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1853
Nucleic Acid Atoms
Solvent Atoms	338
Heterogen Atoms	53

Software

Software
Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.