2F8L | pdb_00002f8l

Crystal structure of a putative class i s-adenosylmethionine-dependent methyltransferase (lmo1582) from listeria monocytogenes at 2.20 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP	8	277	2.4M (NH4)2SO4, 0.1M TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.75	66.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.595	α = 90
b = 99.595	β = 90
c = 117.084	γ = 90

Symmetry
Space Group	I 41

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 210		2005-09-28	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9797, 0.9796, 1.0000	ALS	8.2.1

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	2.2	23.65	99.4	0.072	0.072	7.3	3.7		28765

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	2.2	2.26	99.5	99.5	0.582	0.582	1.2	3.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.2	23.66	27324	1463	99.38	0.168	0.16769	0.165	0.17	0.211	0.21	RANDOM	35.117

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]
0.83			0.83		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.532
r_dihedral_angle_4_deg	23.051
r_dihedral_angle_3_deg	15.488
r_scangle_it	6.946
r_dihedral_angle_1_deg	6.673
r_scbond_it	5.355
r_mcangle_it	3.037
r_mcbond_it	2.012
r_angle_refined_deg	1.585
r_angle_other_deg	0.991
r_mcbond_other	0.527
r_nbd_refined	0.202
r_nbd_other	0.191
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.153
r_symmetry_vdw_other	0.15
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.092
r_nbtor_other	0.086
r_symmetry_vdw_refined	0.04
r_bond_refined_d	0.017
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	2518
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing