5RHO | pdb_00005rho

PanDDA analysis group deposition -- Crystal Structure of Zika virus NS3 Helicase in complex with Z1444783243

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MH3	6mh3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.59	α = 90
b = 69.33	β = 92.12
c = 57.08	γ = 90

Symmetry
Space Group	P 1 21 1

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		2018-09-26		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	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	1.49	57.04	99.5	0.052	0.063	0.034	0.998	10.8	3		67873

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	1.49	1.53	98		0.679	0.882	0.557	0.532		2.2	4933

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	FOURIER SYNTHESIS	THROUGHOUT	6mh3	1.49	57.04	64559	3292	99.47	0.1759	0.1742	0.1776	0.2106	0.2132	RANDOM	23.871

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]
0.06		-0.46	-0.05		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.034
r_dihedral_angle_3_deg	13.912
r_dihedral_angle_4_deg	11.541
r_dihedral_angle_1_deg	6.215
r_mcangle_it	2.938
r_mcbond_it	1.965
r_mcbond_other	1.965
r_angle_refined_deg	1.808
r_angle_other_deg	1.507
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3425
Nucleic Acid Atoms
Solvent Atoms	420
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing