9TPG | pdb_00009tpg

Crystal structure of Zika Virus NS2B-NS3 protease in complex with compound 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LC0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277.15	10% Isopropanol 0.14 M LiSO4 0.10 M Sodium phosphate citrate

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.575	α = 90
b = 91.546	β = 90
c = 103.844	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2020-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999926421265	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.48	68.671	90.9	0.1302	0.1399	0.0502	0.988	9.13	7.72		5729

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.48	2.692	58.7		1.4321	1.5321	0.5391	0.644	1.26	7.77	286

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.48	68.671	5729	269	55.012	0.249	0.247	0.2524	0.2959	0.3013	54.642

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]
-0.641			-1.464		2.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.834
r_dihedral_angle_3_deg	12.295
r_dihedral_angle_6_deg	9.939
r_dihedral_angle_other_3_deg	9.132
r_lrange_it	6.809
r_lrange_other	6.807
r_dihedral_angle_1_deg	5.795
r_mcangle_it	3.552
r_mcangle_other	3.551
r_scangle_it	2.389
r_scangle_other	2.388
r_mcbond_it	1.938
r_mcbond_other	1.932
r_scbond_it	1.265
r_scbond_other	1.264
r_angle_refined_deg	1.075
r_angle_other_deg	0.484
r_nbtor_refined	0.16
r_symmetry_nbd_other	0.155
r_nbd_refined	0.133
r_symmetry_nbd_refined	0.122
r_xyhbond_nbd_refined	0.12
r_nbd_other	0.089
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.047
r_symmetry_xyhbond_nbd_refined	0.025
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1369
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	70

Software

Software
Software Name	Purpose
autoPROC	data processing
autoPROC	data processing
Aimless	data scaling
autoPROC	data processing
REFMAC	refinement
XDS	data reduction
PHASER	phasing