7ZMS

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G4-043

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LB5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2M sodium chloride -- 25% PEG3350 -- 0.1M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.909	α = 90
b = 90.121	β = 90
c = 216.571	γ = 90

Symmetry
Space Group	I 2 2 2

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 PILATUS3 6M		2020-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.17	41.6	99.6	1	7.2	13.3		42737

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.17	2.21			0.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5LB5	2.7	40.988	22465	1151	99.929	0.237	0.235	0.2762	80.715

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]
-0.34			0.293		0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.338
r_dihedral_angle_4_deg	18.954
r_dihedral_angle_3_deg	17.086
r_lrange_it	16.667
r_lrange_other	16.666
r_scangle_it	10.846
r_scangle_other	10.844
r_mcangle_it	10.811
r_mcangle_other	10.811
r_dihedral_angle_1_deg	7.382
r_mcbond_it	7.189
r_mcbond_other	7.18
r_scbond_it	7.045
r_scbond_other	7.045
r_angle_refined_deg	1.555
r_angle_other_deg	1.284
r_symmetry_nbd_refined	0.22
r_nbd_refined	0.213
r_nbd_other	0.208
r_xyhbond_nbd_refined	0.206
r_symmetry_nbd_other	0.202
r_symmetry_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_other	0.127
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.067
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	4335
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing