7HP7 | pdb_00007hp7

PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0014939-001

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	298	30% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8)

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.3	α = 90
b = 42.3	β = 90
c = 216.49	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 EIGER2 XE 9M		2023-10-06		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	1.86	43.3	99.9	0.13	0.133	0.027	0.999	12.2	23.6		17657

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	1.86	1.91		100	6.159	6.301	1.316	0.314		22.2

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 (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	1.86	42.34	16488	853	98.54	0.23011	0.2271	0.2353	0.28637	0.2877	RANDOM	63.471

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]
2.34			2.34		-4.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.353
r_dihedral_angle_3_deg	17.375
r_dihedral_angle_4_deg	16.804
r_long_range_B_refined	10.748
r_long_range_B_other	10.745
r_dihedral_angle_1_deg	7.64
r_scangle_other	3.335
r_mcangle_it	3.254
r_mcangle_other	3.253
r_scbond_it	1.916
r_scbond_other	1.915
r_mcbond_other	1.897
r_mcbond_it	1.853
r_angle_refined_deg	1.792
r_angle_other_deg	1.232
r_chiral_restr	0.072
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.005
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1476
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	56

Software

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