2P3L

Crystal Structure of Dengue Methyltransferase in Complex with GpppA and S-Adenosyl-L-Homocysteine

X-RAY DIFFRACTION

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
2.77	55.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.722	α = 90
b = 108.722	β = 90
c = 55.921	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				2000-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.993	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	2.2	35	99.9	0.061	15.5	3.4	19634	19614			44.91

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	2.2	2.32	99.8		0.382	2.7	3.1	2825

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1L9K	2.2	35	18461	18439	1157	99.88	0.19886	0.19697	0.22761	RANDOM	39.367

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]
-0.07	-0.03		-0.07		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.035
r_dihedral_angle_4_deg	21.685
r_dihedral_angle_3_deg	18.378
r_dihedral_angle_1_deg	5.799
r_scangle_it	2.859
r_scbond_it	1.891
r_angle_refined_deg	1.476
r_mcangle_it	1.309
r_mcbond_it	0.79
r_symmetry_hbond_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.035
r_dihedral_angle_4_deg	21.685
r_dihedral_angle_3_deg	18.378
r_dihedral_angle_1_deg	5.799
r_scangle_it	2.859
r_scbond_it	1.891
r_angle_refined_deg	1.476
r_mcangle_it	1.309
r_mcbond_it	0.79
r_symmetry_hbond_refined	0.304
r_nbtor_refined	0.3
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.191
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2013
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	120

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 National Science Foundation (DBI-1832184), 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 R01GM133198.