2PX2

Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Monoclinic form 1)

X-RAY DIFFRACTION

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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, SITTING DROP		293	0.5mM SAH, 0.2M Calcium chloride, 20% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.4	α = 90
b = 68.3	β = 98.4
c = 82	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 225 mm CCD	mirrors	2005-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97626	ESRF	BM14

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	2	30	92.6	0.071	15.5	3.1		31650		-1.5

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)
	2	2.07	60		0.245	2.6	1.7	2026

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	PDB entry 1L9K	2	27.4	26662	1415	81.66	0.2039	0.20012	0.22	0.27314	0.29	RANDOM	34.372

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]
-1.22		1.02	-2.57		4.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.044
r_dihedral_angle_3_deg	15.391
r_dihedral_angle_4_deg	14.905
r_scangle_it	10.153
r_scbond_it	7.933
r_mcangle_it	5.821
r_mcbond_it	5.67
r_dihedral_angle_1_deg	5.236
r_mcbond_other	1.677
r_angle_refined_deg	1.374
r_angle_other_deg	0.851
r_symmetry_vdw_other	0.254
r_symmetry_hbond_refined	0.227
r_xyhbond_nbd_refined	0.207
r_nbd_refined	0.202
r_nbd_other	0.2
r_symmetry_vdw_refined	0.189
r_nbtor_refined	0.179
r_nbtor_other	0.085
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_bond_other_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4017
Nucleic Acid Atoms
Solvent Atoms	333
Heterogen Atoms	59

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing