3DTN

Crystal structure of putative Methyltransferase-MM_2633 from Methanosarcina mazei .

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	0.1 M Acetate pH 4.5, 30% PEG400, 0.2 M Calcium Acetate monohydrate, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.37	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.276	α = 90
b = 49.94	β = 108.17
c = 77.512	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	ADSC QUANTUM 315		2008-07-05		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9793	APS	24-ID-C

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	2.09	50	95.1	0.076	0.08	21.5	4.6	28850	28850

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.1	2.18	72.6		0.121	0.125	9.5	3.1	2162

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.09	50	28838	1468	94.76	0.189	0.189	0.187	0.234	RANDOM	32.754

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]
-1.66		-0.94	2.59		-1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.071
r_dihedral_angle_4_deg	19.383
r_dihedral_angle_3_deg	17.186
r_dihedral_angle_1_deg	5.743
r_scangle_it	5.058
r_scbond_it	3.179
r_mcangle_it	1.93
r_angle_refined_deg	1.541
r_mcbond_it	1.025
r_chiral_restr	0.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.071
r_dihedral_angle_4_deg	19.383
r_dihedral_angle_3_deg	17.186
r_dihedral_angle_1_deg	5.743
r_scangle_it	5.058
r_scbond_it	3.179
r_mcangle_it	1.93
r_angle_refined_deg	1.541
r_mcbond_it	1.025
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3511
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
CCP4	phasing

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.