7ZMM

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2-001

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	6.5	293	0.2M sodium chloride -- 25% PEG3350 -- 0.1M bis-tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.612	α = 90
b = 183.969	β = 108.124
c = 100.947	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 PILATUS3 6M		2019-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9762	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	2.5	183.84	99.2	1	8.6	2.7		95510

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	2.5	2.55			0.61

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	2.5	95.938	90975	4407	99.371	0.238	0.2356	0.2806	79.866

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]
0.817		-2.886	1.73		-0.541

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.553
r_lrange_other	18.155
r_lrange_it	18.154
r_dihedral_angle_3_deg	16.321
r_dihedral_angle_4_deg	16.143
r_mcangle_it	11.838
r_mcangle_other	11.837
r_scangle_it	11.791
r_scangle_other	11.791
r_mcbond_it	8.053
r_mcbond_other	8.047
r_scbond_it	7.763
r_scbond_other	7.763
r_dihedral_angle_1_deg	6.464
r_angle_refined_deg	1.411
r_angle_other_deg	1.248
r_symmetry_nbd_refined	0.401
r_nbd_other	0.327
r_symmetry_xyhbond_nbd_refined	0.304
r_nbd_refined	0.202
r_symmetry_nbd_other	0.178
r_xyhbond_nbd_refined	0.166
r_nbtor_refined	0.158
r_symmetry_xyhbond_nbd_other	0.143
r_xyhbond_nbd_other	0.124
r_ncsr_local_group_7	0.098
r_ncsr_local_group_11	0.097
r_ncsr_local_group_8	0.094
r_ncsr_local_group_12	0.094
r_ncsr_local_group_6	0.09
r_ncsr_local_group_4	0.088
r_ncsr_local_group_3	0.087
r_ncsr_local_group_2	0.085
r_ncsr_local_group_9	0.085
r_ncsr_local_group_10	0.083
r_ncsr_local_group_1	0.081
r_ncsr_local_group_5	0.081
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.06
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	17546
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms

Software

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