4GOL | pdb_00004gol

Crystal Structure of E. coli DNA Adenine Methyltransferase in Complex with Methylated Aza-SAM

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	100 mM MES, 1600 mM ammonium Sulfate, 14-18% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.97	α = 90
b = 160.97	β = 90
c = 96.029	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	ADSC QUANTUM 315r		2010-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.924530	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.539	35.873	99.9	0.077	18.1	6.2	47602	47602

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	2.54	2.6	100		0.781	0.781	1	6.2	3489

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.57	29.09	45751	2263	99.94	0.2107	0.2088	0.2	0.2479	0.24	RANDOM	44.5173

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37
r_dihedral_angle_4_deg	18.936
r_dihedral_angle_3_deg	17.204
r_dihedral_angle_1_deg	7.328
r_scangle_it	5.287
r_scbond_it	3.302
r_mcangle_it	2.336
r_angle_refined_deg	1.941
r_mcbond_it	1.233
r_chiral_restr	0.129

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37
r_dihedral_angle_4_deg	18.936
r_dihedral_angle_3_deg	17.204
r_dihedral_angle_1_deg	7.328
r_scangle_it	5.287
r_scbond_it	3.302
r_mcangle_it	2.336
r_angle_refined_deg	1.941
r_mcbond_it	1.233
r_chiral_restr	0.129
r_bond_refined_d	0.023
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6039
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	81

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.