2P41 | pdb_00002p41

Crystal Structure of Dengue Methyltransferase in Complex with 7MeGpppG2'OMe and S-Adenosyl-L-homocysteine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L9K	PDB ENTRY 1L9K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	293	0.4 M Ammonium Sulfate, 0.1 M Sodium Citrate, 1.2 M Lithium Sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.394	α = 90
b = 108.394	β = 90
c = 55.89	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				2002-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

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	1.8	38.9	99.5	0.034	37.6	6.9	35292	35115			25.71

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	97.3		0.215	6.1	4.2	4976

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	PDB ENTRY 1L9K	1.801	36.66	33164	32998	2070	99.5	0.16469	0.16469	0.16271	0.16	0.19588	0.19	RANDOM	29.058

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]
0.32	0.16		0.32		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.063
r_dihedral_angle_4_deg	16.366
r_dihedral_angle_3_deg	13.467
r_dihedral_angle_1_deg	5.26
r_scangle_it	2.922
r_scbond_it	1.918
r_angle_refined_deg	1.542
r_mcangle_it	1.15
r_mcbond_it	0.797
r_symmetry_hbond_refined	0.385

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.063
r_dihedral_angle_4_deg	16.366
r_dihedral_angle_3_deg	13.467
r_dihedral_angle_1_deg	5.26
r_scangle_it	2.922
r_scbond_it	1.918
r_angle_refined_deg	1.542
r_mcangle_it	1.15
r_mcbond_it	0.797
r_symmetry_hbond_refined	0.385
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.261
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.114
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2026
Nucleic Acid Atoms
Solvent Atoms	302
Heterogen Atoms	145

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.