5RMC | pdb_00005rmc

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 helicase in complex with Z24758179

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	47.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.219	α = 102.52
b = 70.236	β = 96.43
c = 85.632	γ = 112.39

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		2020-07-31		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	2.15	81.51	97.2	0.109	0.131	0.07	0.994	7.5	3.4		64437

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	2.15	2.2	95.3		1.717	2.059	1.118	0.41		3.4	4544

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	2.15	81.63	60959	3333	96.8	0.2115	0.2089	0.22	0.2575	0.27	RANDOM	54.574

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]
0.36	-1.07	-2.44	-2.99	-0.16	4.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.112
r_dihedral_angle_3_deg	16.011
r_dihedral_angle_4_deg	15.998
r_dihedral_angle_1_deg	6.413
r_mcangle_it	5.981
r_mcbond_it	3.766
r_mcbond_other	3.765
r_angle_refined_deg	1.437
r_angle_other_deg	1.244
r_chiral_restr	0.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.112
r_dihedral_angle_3_deg	16.011
r_dihedral_angle_4_deg	15.998
r_dihedral_angle_1_deg	6.413
r_mcangle_it	5.981
r_mcbond_it	3.766
r_mcbond_other	3.765
r_angle_refined_deg	1.437
r_angle_other_deg	1.244
r_chiral_restr	0.062
r_bond_refined_d	0.006
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	455
Heterogen Atoms	41

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.