9RM4 | pdb_00009rm4

Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0015373

X-RAY DIFFRACTION

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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		298	30% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8)

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.42	α = 90
b = 42.42	β = 90
c = 215.96	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		2023-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92124	Diamond	I04-1

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	1.95	42.456	100	0.118	0.124	0.04	0.999	13.9	17		15473

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)
1	1.95	2			2.994	3.158	1	0.654		18.2

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	1.95	42.456	15393	786	99.968	0.218	0.2152	0.214	0.2782	0.2796	48.782

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]
1.264			1.264		-2.529

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.588
r_dihedral_angle_4_deg	23.082
r_dihedral_angle_3_deg	15.83
r_dihedral_angle_1_deg	7.956
r_lrange_it	5.273
r_lrange_other	5.272
r_scangle_it	2.756
r_scangle_other	2.754
r_mcangle_it	2.294
r_mcangle_other	2.293
r_scbond_it	1.741
r_scbond_other	1.74
r_angle_refined_deg	1.586
r_mcbond_it	1.443
r_mcbond_other	1.436
r_angle_other_deg	1.267
r_nbd_other	0.203
r_nbd_refined	0.186
r_symmetry_nbd_other	0.185
r_xyhbond_nbd_refined	0.167
r_nbtor_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.138
r_symmetry_nbd_refined	0.117
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_symmetry_xyhbond_nbd_other	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	1438
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	28

Software

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