8TBX

Crystal structure of human DDX1 helicase in complex with ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AlphaFold model is used with PHASER

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.04M Potassium phosphate monobasic,16%w/v PEG 8K,20% v/v Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.708	α = 90
b = 71.517	β = 90
c = 138.496	γ = 90

Symmetry
Space Group	P 21 21 21

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 X 16M		2023-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97911	APS	24-ID-C

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	2.7	50	99.9	0.151	0.163	0.061	0.995	5	7.1		14191

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	2.7	2.75	100		0.967	1.046	0.392	0.753		6.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.71	49.8	13419	728	99.47	0.20678	0.20257	0.28647	RANDOM	47.552

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]
1.65			-2.52		0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.354
r_dihedral_angle_4_deg	19.979
r_dihedral_angle_3_deg	17.889
r_long_range_B_refined	9.415
r_long_range_B_other	9.414
r_dihedral_angle_1_deg	7.414
r_mcangle_it	6.361
r_mcangle_other	6.36
r_scangle_other	6.304
r_mcbond_other	4.158
r_mcbond_it	4.157
r_scbond_it	4.081
r_scbond_other	4.081
r_angle_refined_deg	1.374
r_angle_other_deg	1.215
r_chiral_restr	0.053
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001
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	3435
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PHASER	phasing
HKL-3000	data reduction