9RM7 | pdb_00009rm7

Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0036543

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8PN6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	30% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8)

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.484	α = 90
b = 42.484	β = 90
c = 218.029	γ = 90

Symmetry
Space Group	P 43 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 EIGER X 9M		2025-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9212	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.45	54.567	100	1	24.9	1.8		36991

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.47			0.714		1.9

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	1.45	54.567	36879	1863	99.957	0.196	0.1945	0.1911	0.2222	0.2176	30.58

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]
0.914			0.914		-1.829

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.698
r_dihedral_angle_4_deg	15.021
r_dihedral_angle_3_deg	11.412
r_dihedral_angle_1_deg	7.867
r_lrange_it	4.958
r_lrange_other	4.842
r_scangle_it	2.941
r_scangle_other	2.94
r_scbond_it	1.954
r_scbond_other	1.953
r_mcangle_other	1.759
r_mcangle_it	1.758
r_angle_refined_deg	1.741
r_angle_other_deg	1.469
r_mcbond_it	1.189
r_mcbond_other	1.176
r_symmetry_xyhbond_nbd_refined	0.237
r_nbd_other	0.212
r_symmetry_nbd_refined	0.208
r_nbd_refined	0.187
r_symmetry_nbd_other	0.185
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.161
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.007
r_chiral_restr_other	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1444
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
PHASER	phasing