2O57

Crystal Structure of a putative sarcosine dimethylglycine methyltransferase from Galdieria sulphuraria

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Protein Solution (10 MG/ML protein, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, 0.005 M Bis Tris pH 7.0) mixed in a 1:1 ratio with the Well Solution (23% MEPEG 5K, 0.03 M sarcosine, 0.1 M MOPS pH 7.0), Cryoprotected with: well solution supplemented with up to 15% glycerol, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.541	α = 90
b = 291.433	β = 90
c = 86.34	γ = 90

Symmetry
Space Group	C 2 2 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	Adjustable focusing mirrors in K-B geometry	2006-11-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97923, 0.96400	APS	23-ID-D

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	1.95	50	99.4	0.11	7.618	7.2		89709

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)
	1.95	2.02	95		0.597	1.775	5.1	8471

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.946	48.771	89679	4502	99.242	0.168	0.166	0.221	RANDOM	21.559

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]
0.295			-0.701		0.406

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.257
r_dihedral_angle_4_deg	19.467
r_dihedral_angle_3_deg	13.913
r_dihedral_angle_1_deg	6.026
r_scangle_it	3.445
r_scbond_it	2.305
r_angle_refined_deg	1.452
r_mcangle_it	1.352
r_mcbond_it	0.848
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.257
r_dihedral_angle_4_deg	19.467
r_dihedral_angle_3_deg	13.913
r_dihedral_angle_1_deg	6.026
r_scangle_it	3.445
r_scbond_it	2.305
r_angle_refined_deg	1.452
r_mcangle_it	1.352
r_mcbond_it	0.848
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.206
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.141
r_chiral_restr	0.105
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8744
Nucleic Acid Atoms
Solvent Atoms	1042
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.