3RC5 | pdb_00003rc5

Molecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M5M	PDB ID 3M5M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop, vapor diffusion	6.5	295	20-25% PEG 3350, 0.1M MES (pH 6.5), 4% ammonium sulfate, hanging drop, vapor diffusion, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.096	α = 90
b = 58.21	β = 90
c = 61.325	γ = 90

Symmetry
Space Group	P 21 21 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				2010-08-05		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	1.6	50	99.3	0.039	18.8	3.7		26041

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)
	1.6	1.66	99.1		0.23		3.7	2566

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 ID 3M5M	1.6	27.05	25918	1310	98.95	0.1725	0.1714	0.2	0.1929	0.22	RANDOM	28.1905

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]
0.49			-1.27		0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.002
r_dihedral_angle_4_deg	16.891
r_dihedral_angle_3_deg	12.655
r_dihedral_angle_1_deg	6.187
r_scangle_it	2.704
r_scbond_it	1.665
r_angle_refined_deg	1.26
r_mcangle_it	1.093
r_angle_other_deg	0.82
r_mcbond_it	0.598

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.002
r_dihedral_angle_4_deg	16.891
r_dihedral_angle_3_deg	12.655
r_dihedral_angle_1_deg	6.187
r_scangle_it	2.704
r_scbond_it	1.665
r_angle_refined_deg	1.26
r_mcangle_it	1.093
r_angle_other_deg	0.82
r_mcbond_it	0.598
r_mcbond_other	0.159
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1502
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	11

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.