5RLG | pdb_00005rlg

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z19739650

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	16 % Ethylene Glycol, 8 % PEG 8K, 0.05 M HEPES, 0.05 M MOPS, 0.03 M Sodium Nitrate, 0,03 M Sodium Phosphate, 0.03 M Ammonium Sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.184	α = 103.01
b = 70.314	β = 96.26
c = 85.682	γ = 112.07

Symmetry
Space Group	P 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		2020-07-29		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9126	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	1.96	81.56	96.4	0.089	0.105	0.056	0.998	6.8	3.4		84285

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	1.96	2	90.4		2.053	2.486	1.375	0.293		3.1	4175

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	6ZSL	1.96	81.54	77969	4222	94.05	0.2479	0.2458	0.26	0.2859	0.3	RANDOM	53.01

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]
0.67	-0.59	-2.57	-2.09	-0.53	3.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.314
r_dihedral_angle_4_deg	17.577
r_dihedral_angle_3_deg	14.38
r_dihedral_angle_1_deg	7.297
r_mcangle_it	6.992
r_mcbond_other	4.532
r_mcbond_it	4.531
r_angle_refined_deg	1.52
r_angle_other_deg	1.249
r_chiral_restr	0.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.314
r_dihedral_angle_4_deg	17.577
r_dihedral_angle_3_deg	14.38
r_dihedral_angle_1_deg	7.297
r_mcangle_it	6.992
r_mcbond_other	4.532
r_mcbond_it	4.531
r_angle_refined_deg	1.52
r_angle_other_deg	1.249
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	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	8917
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	40

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.