2PCN | pdb_00002pcn

Crystal structure of S-adenosylmethionine: 2-dimethylmenaquinone methyltransferase (gk_1813) from geobacillus kaustophilus HTA426

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NXJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	OIL BATCH METHOD	6.5	293	0.1M SODIUM CACODYLATE TRIHYDRATE, 1.4M SODIUM ACETATE TRIHYDRATE, pH 6.5, OIL BATCH METHOD, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.573	α = 90
b = 84.573	β = 90
c = 83.338	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS V	RH COATED BENT-CYRINDRICAL MIRROR	2006-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45PX	1.0	SPring-8	BL45PX

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	1.9	40	99.8	0.075	0.084				17473			13.1

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	1.9	1.97	99.9		0.21	0.204			1747

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1NXJ	1.9	36.22	17396	1720	99.3	0.176	0.176	0.17	0.205	0.2	RANDOM	22.2

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]
1.92	1.96		1.92		-3.84

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.6
c_scangle_it	6.25
c_scbond_it	4.41
c_mcangle_it	3.3
c_mcbond_it	2.66
c_angle_deg	1.3
c_improper_angle_d	0.72
c_bond_d	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1193
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	4

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

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.