7ZMO

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-052

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	293	1M ammonium sulfate -- 0.5% PEG8000 -- 0.1M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
6.25	80.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.517	α = 90
b = 150.87	β = 90
c = 269.342	γ = 90

Symmetry
Space Group	P 2 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 PILATUS3 6M		2020-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9119	Diamond	I04-1

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	3.03	100.67	100	1	2.5	6.7		71635

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	3.03	3.08	100		0.1

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	3.75	100.67	38213	1891	99.854	0.284	0.2832	0.3063	127.165

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]
1.068			-1.935		0.867

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	31.289
r_lrange_other	31.289
r_dihedral_angle_2_deg	27.897
r_mcangle_it	21.087
r_mcangle_other	21.085
r_scangle_it	18.636
r_scangle_other	18.635
r_dihedral_angle_3_deg	17.588
r_dihedral_angle_4_deg	15.215
r_mcbond_it	13.318
r_mcbond_other	13.317
r_scbond_it	11.181
r_scbond_other	11.18
r_dihedral_angle_1_deg	7.793
r_angle_refined_deg	1.794
r_angle_other_deg	1.365
r_symmetry_xyhbond_nbd_refined	0.484
r_nbd_other	0.405
r_symmetry_nbd_refined	0.389
r_nbd_refined	0.232
r_symmetry_nbd_other	0.219
r_symmetry_xyhbond_nbd_other	0.175
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.168
r_ncsr_local_group_1	0.122
r_ncsr_local_group_2	0.113
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_xyhbond_nbd_other	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8550
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	10

Software

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