3D2L | pdb_00003d2l

Crystal structure of SAM-dependent methyltransferase (ZP_00538691.1) from EXIGUOBACTERIUM SP. 255-15 at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.2000M MgCl2, 20.0000% PEG-8000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.83	α = 116.57
b = 70.92	β = 104.63
c = 77.19	γ = 102.32

Symmetry
Space Group	P 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)	2008-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		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	1.9	29.374	92.2	0.051	14.73	7.86		84662		-3	30.367

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	1.9	1.97	63.7		0.649	2.28

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.9	29.374	84658	4235	93.02	0.189	0.187	0.19	0.229	0.23	RANDOM	28.362

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]
2.03	0.45	1.72	-1.37	-0.17	0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.668
r_dihedral_angle_4_deg	17.391
r_dihedral_angle_3_deg	11.583
r_scangle_it	6.083
r_scbond_it	4.681
r_dihedral_angle_1_deg	3.743
r_mcangle_it	2.546
r_mcbond_it	1.841
r_angle_refined_deg	1.587
r_angle_other_deg	0.933
r_mcbond_other	0.647
r_symmetry_vdw_other	0.297
r_nbd_refined	0.214
r_nbd_other	0.195
r_nbtor_refined	0.182
r_symmetry_vdw_refined	0.156
r_xyhbond_nbd_refined	0.154
r_xyhbond_nbd_other	0.148
r_symmetry_hbond_refined	0.144
r_metal_ion_refined	0.103
r_chiral_restr	0.095
r_nbtor_other	0.089
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	7631
Nucleic Acid Atoms
Solvent Atoms	516
Heterogen Atoms	6

Software

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