2P8J | pdb_00002p8j

Crystal structure of S-adenosylmethionine-dependent methyltransferase (NP_349143.1) from Clostridium acetobutylicum at 2.00 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	277	NANODROP, 0.2M (NH4)2SO4, 10.0% Glycerol, 20.0% PEG 300, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.31	62.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.86	α = 90
b = 83.86	β = 90
c = 159.2	γ = 120

Symmetry
Space Group	P 31 2 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-01-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91162, 0.97908, 0.97879	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	2	29.975	99.6	0.044	21.1	4.9		44338			32.8

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	2	2.05	99.6		0.325	3.09	4.9	3115

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	29.16	44263	2229	99.53	0.167	0.167	0.165	0.18	0.201	0.21	RANDOM	43.522

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]
-0.17	-0.08		-0.17		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.632
r_dihedral_angle_4_deg	15.593
r_dihedral_angle_3_deg	12.552
r_dihedral_angle_1_deg	6.653
r_scangle_it	6.477
r_scbond_it	4.761
r_mcangle_it	2.677
r_mcbond_it	1.881
r_angle_refined_deg	1.352
r_angle_other_deg	0.78
r_mcbond_other	0.588
r_symmetry_vdw_refined	0.226
r_symmetry_vdw_other	0.192
r_nbd_refined	0.188
r_symmetry_hbond_refined	0.186
r_nbd_other	0.183
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.084
r_nbtor_other	0.084
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3287
Nucleic Acid Atoms
Solvent Atoms	318
Heterogen Atoms	88

Software

Software
Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
SHELXD	phasing
autoSHARP	phasing