5RHY | pdb_00005rhy

PanDDA analysis group deposition of ground-state model of Zika Virus NS3 Helicase

X-RAY DIFFRACTION

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	42.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.461	α = 90
b = 69.011	β = 92.05
c = 57.222	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 2M		2018-09-29		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.91587	Diamond	I02

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	1.36	57.19	96.1	0.039	0.046	0.025	0.999	12.5	2.8		86412

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	1.36	1.43	78.3		0.737	0.983	0.644	0.472		1.6	10248

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	1.36	57.25	82144	4245	96.01	0.1721	0.1705	0.18	0.2049	0.21	RANDOM	21.833

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]
0.08		-0.02	-0.14		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.989
r_dihedral_angle_3_deg	12.711
r_dihedral_angle_4_deg	12.509
r_dihedral_angle_1_deg	5.984
r_mcangle_it	3.029
r_angle_refined_deg	2.255
r_mcbond_other	2.117
r_mcbond_it	2.116
r_angle_other_deg	1.173
r_chiral_restr	0.162

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.989
r_dihedral_angle_3_deg	12.711
r_dihedral_angle_4_deg	12.509
r_dihedral_angle_1_deg	5.984
r_mcangle_it	3.029
r_angle_refined_deg	2.255
r_mcbond_other	2.117
r_mcbond_it	2.116
r_angle_other_deg	1.173
r_chiral_restr	0.162
r_bond_refined_d	0.024
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3425
Nucleic Acid Atoms
Solvent Atoms	421
Heterogen Atoms	22

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.