4IV8 | pdb_00004iv8

Crystal structure of N-methyl transferase from Plasmodium knowlesi complexed with S-adenosyl methionine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UJ7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	282	Protein solution was at 15 mg/mL containing 20 mM Tris, 100 mM NaCl, 2 mM EDTA and 5 mM bME, 5 mM SAM. Mother liqueur contained 0.1 M Na-acetate (pH 5.0) and 20% PEG 3.350. Cryoprotectant was 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 282K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.71	α = 90
b = 96.76	β = 90
c = 38.46	γ = 90

Symmetry
Space Group	P 21 21 2

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	RAYONIX MX-300		2012-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	20	99.8	0.089	12.81		51102	51018		-3	30.857

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	1.95	100		0.748	2.56

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	3UJ7	1.9	19.7	51016	50979	2549	99.83	0.253	0.2347	0.2328	0.23	0.2708	0.27	RANDOM	27.0975

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]
-0.09			0.03		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.762
r_dihedral_angle_3_deg	13.938
r_dihedral_angle_4_deg	10.74
r_dihedral_angle_1_deg	5.082
r_angle_refined_deg	1.147
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4048
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	62

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
PHASER	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.