3FQM | pdb_00003fqm

Crystal structure of a novel dimeric form of HCV NS5A domain I protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZH1	Monomer from 1ZH1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	22% PEG-3350, 0.1 M HEPES pH 7.5, 10% (v/v) isopropanol, N-nonylphosphocholine (FOS-CHOLINE-9 from Hampton screen 3, No. 18), VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.165	α = 90
b = 57.165	β = 90
c = 195.385	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	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	1.9	34.77	99.3	0.054	0.054	44	7.1	30054	30054			32

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	1.9	2	98.6		0.398	0.398	3.6	6.7	2912

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	Monomer from 1ZH1	1.9	34.77	29345	29345	626	99.26	0.248	0.248	0.247	0.24	0.288	0.28	RANDOM	33.996

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]
0.4	0.2		0.4		-0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.421
r_dihedral_angle_4_deg	17.573
r_dihedral_angle_3_deg	15.961
r_dihedral_angle_1_deg	5.725
r_scangle_it	2.413
r_scbond_it	1.615
r_angle_refined_deg	1.222
r_mcangle_it	1.201
r_mcbond_it	0.699
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.225
r_symmetry_hbond_refined	0.199
r_nbd_refined	0.194
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2466
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms	8

Software

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