7ZMV

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 232.589	α = 90
b = 89.965	β = 110.058
c = 164.126	γ = 90

Symmetry
Space Group	C 1 2 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		2021-02-12	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	2	109.23	97.7	1	13.9	2.9		209231

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	2.04	87.3		0.3

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	2.002	77.687	208891	10399	97.572	0.245	0.2431	0.2747	48.403

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]
0.018		0.005	-0.02		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.17
r_dihedral_angle_4_deg	17.464
r_dihedral_angle_3_deg	16.197
r_lrange_other	10.892
r_lrange_it	10.888
r_scangle_it	7.681
r_scangle_other	7.672
r_dihedral_angle_1_deg	6.856
r_mcangle_it	5.958
r_mcangle_other	5.958
r_scbond_it	5.121
r_scbond_other	5.084
r_mcbond_it	4.158
r_mcbond_other	4.158
r_angle_refined_deg	1.443
r_angle_other_deg	1.334
r_symmetry_nbd_refined	0.254
r_nbd_other	0.219
r_nbd_refined	0.202
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.145
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_9	0.078
r_ncsr_local_group_11	0.07
r_ncsr_local_group_8	0.069
r_chiral_restr	0.065
r_ncsr_local_group_5	0.062
r_ncsr_local_group_10	0.061
r_ncsr_local_group_12	0.061
r_ncsr_local_group_3	0.059
r_ncsr_local_group_1	0.058
r_ncsr_local_group_7	0.058
r_ncsr_local_group_2	0.056
r_ncsr_local_group_6	0.056
r_ncsr_local_group_4	0.054
r_symmetry_xyhbond_nbd_other	0.035
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17422
Nucleic Acid Atoms
Solvent Atoms	1028
Heterogen Atoms	20

Software

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