2P7I

CRYSTAL STRUCTURE OF a SAM dependent methyl-transferase type 12 family protein (ECA1738) FROM PECTOBACTERIUM ATROSEPTICUM SCRI1043 AT 1.74 A RESOLUTION

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	NANODROP, 64.4% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.83	α = 90
b = 120.83	β = 90
c = 149.967	γ = 90

Symmetry
Space Group	I 4 2 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 325 mm CCD	Flat mirror (vertical focusing)	2007-03-02	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97899, 0.97925	SSRL	BL11-1

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	1.74	29.111	100	0.09	0.09	6.3	7.3		56875			25.14

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)
1	1.74	1.79	100		0.011	1.108	0.7	7.4	4169

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	MAD	THROUGHOUT	1.74	29.111	56875	2883	99.92	0.156	0.156	0.155	0.18	RANDOM	26.628

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]
1.35			1.35		-2.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.528
r_dihedral_angle_3_deg	13.212
r_dihedral_angle_4_deg	12.778
r_scangle_it	6.885
r_dihedral_angle_1_deg	5.883
r_scbond_it	4.692
r_mcangle_it	2.829
r_mcbond_it	1.734
r_angle_refined_deg	1.45
r_angle_other_deg	0.9
r_mcbond_other	0.71
r_symmetry_vdw_refined	0.322
r_symmetry_vdw_other	0.276
r_nbd_refined	0.216
r_nbd_other	0.198
r_nbtor_refined	0.188
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.142
r_metal_ion_refined	0.109
r_chiral_restr	0.091
r_nbtor_other	0.087
r_symmetry_metal_ion_refined	0.067
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3616
Nucleic Acid Atoms
Solvent Atoms	366
Heterogen Atoms	26

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing
autoSHARP	phasing