3E8S

Crystal structure of Putative SAM Dependent Methyltransferase in Complex with SAH (NP_744700.1) from PSEUDOMONAS PUTIDA KT2440 at 2.10 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	3.6M sodium formate, 10.0% Glycerol, Additive 0.001 M S-adenosylmethionine (SAM), VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
5.3	76.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.433	α = 90
b = 130.433	β = 90
c = 54.431	γ = 120

Symmetry
Space Group	P 64

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)	2008-08-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97920,0.97845	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	2.1	28.239	99.9	0.068	8.039	5.6		31089			38.343

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	2.1	2.15	100		0.521	1.5	5.6

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	2.1	28.239	31072	1568	99.88	0.159	0.158	0.176	RANDOM	46.049

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]
-1.63	-0.82		-1.63		2.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.91
r_dihedral_angle_4_deg	18.651
r_dihedral_angle_3_deg	10.759
r_scangle_it	7.107
r_scbond_it	5.234
r_dihedral_angle_1_deg	3.779
r_mcangle_it	3.079
r_mcbond_it	2.364
r_angle_refined_deg	1.637
r_angle_other_deg	1
r_mcbond_other	0.55
r_symmetry_vdw_other	0.323
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.218
r_nbd_other	0.202
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.178
r_symmetry_hbond_refined	0.175
r_chiral_restr	0.099
r_nbtor_other	0.087
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1699
Nucleic Acid Atoms
Solvent Atoms	219
Heterogen Atoms	26

Software

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