7ZML

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G1-001

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	293	0.1M bis-tris pH 5.9 -- 0.1M lithium sulfate -- 30% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.74	α = 90
b = 185.53	β = 107.47
c = 101.01	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		2018-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.79	96.351	99.8	0.083	1	12.9	6.8		65889

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	2.79	2.84			0.5	1.1

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	2.79	96.351	65750	3147	99.58	0.226	0.2238	0.261	103.124

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]
-2.819		-2.55	0.1		3.609

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.827
r_lrange_it	23.509
r_lrange_other	23.509
r_dihedral_angle_4_deg	17.924
r_dihedral_angle_3_deg	16.808
r_scangle_it	16.126
r_scangle_other	16.091
r_mcangle_it	15.776
r_mcangle_other	15.776
r_mcbond_it	10.956
r_mcbond_other	10.949
r_scbond_it	10.803
r_scbond_other	10.766
r_dihedral_angle_1_deg	6.843
r_angle_refined_deg	1.432
r_angle_other_deg	1.237
r_nbd_other	0.313
r_symmetry_nbd_refined	0.298
r_symmetry_xyhbond_nbd_refined	0.29
r_nbd_refined	0.204
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.146
r_ncsr_local_group_12	0.118
r_ncsr_local_group_8	0.11
r_ncsr_local_group_10	0.101
r_ncsr_local_group_9	0.096
r_ncsr_local_group_11	0.087
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_3	0.077
r_ncsr_local_group_2	0.075
r_ncsr_local_group_6	0.074
r_ncsr_local_group_1	0.071
r_ncsr_local_group_5	0.068
r_ncsr_local_group_4	0.064
r_ncsr_local_group_7	0.063
r_chiral_restr	0.059
r_symmetry_xyhbond_nbd_other	0.046
r_bond_refined_d	0.007
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	17587
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	20

Software

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