4GHA | pdb_00004gha

Crystal structure of Marburg virus VP35 RNA binding domain bound to 12-bp dsRNA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GH9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1 M Bis-Tris, 2% v/v Tacsimate, 18% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.593	α = 90
b = 99.191	β = 89.92
c = 81.801	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	77	CCD	ADSC QUANTUM 315r	Double-crystal, Si(111) liquid N2 cooled	2011-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.0000	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	81.8		0.131	0.131	8.5	2.5		20261	1	1	17

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.501	2.566	100		0.362	0.362	2.2	2.5	988

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	4GH9	2.5	81.8	1	1	18981	1017	98.7	0.21073	0.21073	0.20867	0.21	0.24987	0.25	RANDOM	17

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]
0.12		0.36	-1.3		1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.227
r_dihedral_angle_3_deg	9.955
r_dihedral_angle_4_deg	9.247
r_dihedral_angle_1_deg	2.748
r_scangle_it	1.541
r_mcangle_it	1.153
r_scbond_it	0.845
r_mcbond_it	0.632
r_rigid_bond_restr	0.561
r_angle_refined_deg	0.448
r_chiral_restr	0.028
r_bond_refined_d	0.001
r_gen_planes_refined	0.001
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3772
Nucleic Acid Atoms	504
Solvent Atoms	156
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling