3DLC

Crystal structure of a putative s-adenosyl-l-methionine-dependent methyltransferase (mmp1179) from methanococcus maripaludis at 1.15 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	0.17M ammonium acetate, 15.0% Glycerol, 25.5% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, Additive - 1mM S-adenosylmethionine, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.61	α = 90
b = 63.5	β = 90
c = 75.44	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 325 mm CCD	Flat mirror (vertical focusing)	2008-06-15	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97947	SSRL	BL11-1

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	1.15	29.26	98	0.037	11.43			68022		-3	7.892

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	1.15	1.19	94.2		0.378	2.3

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	1.15	29.26	67971	3439	99.46	0.121	0.12	0.138	RANDOM	9.085

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]
0.62			0.16		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.038
r_dihedral_angle_4_deg	17.48
r_dihedral_angle_3_deg	11.665
r_sphericity_free	7.559
r_scangle_it	5.12
r_dihedral_angle_1_deg	4.988
r_scbond_it	3.919
r_sphericity_bonded	3.369
r_mcangle_it	2.575
r_rigid_bond_restr	2.217
r_mcbond_it	1.776
r_angle_refined_deg	1.723
r_angle_other_deg	1.342
r_mcbond_other	0.856
r_chiral_restr	0.114
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1722
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing