4YYC | pdb_00004yyc

Crystal structure of trimethylamine methyltransferase from Sinorhizobium meliloti in complex with unknown ligand

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	0.2 ul of 14 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-I condition #33 (32%w/v PEG 4K, 0.1M Tris HCl, 0.8 M Lithium Chloride, pH=8.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was mixed with 1/15 v/v of 1 mg/ml TEV protease solution

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.162	α = 90
b = 60.025	β = 90
c = 88.345	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 300 mm CCD	Bimorph K-B pair	2014-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07808	APS	21-ID-D

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	1.56	50	99.3	0.052	0.052	0.059	0.027	10.3	4.6		67995		-3	19

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	1.56	1.59	97.4		0.615	0.71	0.344	0.806	1.9	3.8	3289

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	1.56	50	64442	3363	99.36	0.1403	0.1391	0.15	0.1654	0.17	RANDOM	23.702

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]
-1.22			1.01		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.937
r_dihedral_angle_4_deg	17.396
r_dihedral_angle_3_deg	11.922
r_dihedral_angle_1_deg	6.23
r_angle_refined_deg	1.563
r_mcangle_it	1.036
r_angle_other_deg	0.96
r_mcbond_it	0.625
r_mcbond_other	0.623
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.937
r_dihedral_angle_4_deg	17.396
r_dihedral_angle_3_deg	11.922
r_dihedral_angle_1_deg	6.23
r_angle_refined_deg	1.563
r_mcangle_it	1.036
r_angle_other_deg	0.96
r_mcbond_it	0.625
r_mcbond_other	0.623
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3651
Nucleic Acid Atoms
Solvent Atoms	530
Heterogen Atoms	8

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
Coot	model building
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.