2J7U | pdb_00002j7u

Dengue virus NS5 RNA dependent RNA polymerase domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HFZ	PDB ENTRY 2HFZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		0.1 M TRIS-HCL PH 8.5, 0.8M K/NA TARTRATE, 0.5% W/V PEG MME 5K.

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.15	α = 90
b = 180.478	β = 90
c = 57.987	γ = 90

Symmetry
Space Group	C 2 2 21

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	MARRESEARCH	MIRRORS	2006-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	1.85	48	99.9	0.01	14.62	4.9		72065

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	1.85	1.93	99.9		0.54	2.98	4.9

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 2HFZ	1.85	20	68360	3646	99.9	0.201	0.2	0.2	0.234	0.2	RANDOM	36.72

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]
-0.97			2.23		-1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.979
r_dihedral_angle_4_deg	15.995
r_dihedral_angle_3_deg	13.633
r_dihedral_angle_1_deg	4.59
r_scangle_it	1.487
r_scbond_it	0.92
r_angle_refined_deg	0.919
r_mcangle_it	0.602
r_mcbond_it	0.351
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.176
r_nbd_refined	0.175
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4642
Nucleic Acid Atoms
Solvent Atoms	505
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
AMoRE	phasing