3KHK | pdb_00003khk

Crystal structure of type-I restriction-modification system methylation subunit (MM_0429) from Methanosarchina mazei.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	Sodium acetate trihydrate pH 4.6, 25% PEG 3350,0.2M Ammonium Acetate,0.05M Magnesium Sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.648	α = 90
b = 80.648	β = 90
c = 179.973	γ = 90

Symmetry
Space Group	P 41

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 315		2009-08-20		SINGLE WAVELENGTH
2	1	100	CCD	ADSC QUANTUM 315		2009-03-06

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9793	NSLS	X29A
2	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.979	APS	24-ID-C

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	2.5	25	100	0.098	0.117	25.8	10.6	37205	37205

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)
	2.55	2.59	100		0.816	0.882	3	10.7	1916

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	2.55	25	37097	1858	99.65	0.214	0.213	0.21	0.242	0.23	RANDOM	51.862

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]
5.82			5.82		-11.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.963
r_dihedral_angle_4_deg	19.83
r_dihedral_angle_3_deg	19.287
r_dihedral_angle_1_deg	6.458
r_scangle_it	2.204
r_scbond_it	1.424
r_angle_refined_deg	1.355
r_mcangle_it	1.018
r_mcbond_it	0.545
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.963
r_dihedral_angle_4_deg	19.83
r_dihedral_angle_3_deg	19.287
r_dihedral_angle_1_deg	6.458
r_scangle_it	2.204
r_scbond_it	1.424
r_angle_refined_deg	1.355
r_mcangle_it	1.018
r_mcbond_it	0.545
r_chiral_restr	0.097
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7863
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
SHELXD	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.