7ZMN | pdb_00007zmn

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-048

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		293	2M ammonium sulfate -- 0.1M HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
3.67	66.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.503	α = 90
b = 89.573	β = 90
c = 259.056	γ = 90

Symmetry
Space Group	P 2 2 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	2.74	129.63	99.6	1	4.8	6.6		49418

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	2.74	2.79			0.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5LB5	3.2	129.528	31267	1559	99.535	0.244	0.2419	0.24	0.2746	0.27	69.309

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]
-0.01			-0.037		0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.083
r_dihedral_angle_3_deg	17.994
r_dihedral_angle_4_deg	16.607
r_lrange_other	12.142
r_lrange_it	12.141
r_mcangle_it	8.375
r_mcangle_other	8.374
r_scangle_other	8.245
r_scangle_it	8.239
r_dihedral_angle_1_deg	7.333
r_mcbond_it	5.196
r_mcbond_other	5.195
r_scbond_other	4.988
r_scbond_it	4.985
r_angle_refined_deg	1.54
r_angle_other_deg	1.262
r_nbd_other	0.246
r_symmetry_xyhbond_nbd_refined	0.229
r_nbd_refined	0.213
r_symmetry_nbd_other	0.206
r_symmetry_nbd_refined	0.196
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.146
r_ncsr_local_group_1	0.089
r_symmetry_nbtor_other	0.085
r_ncsr_local_group_2	0.069
r_chiral_restr	0.063
r_symmetry_xyhbond_nbd_other	0.047
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8686
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	17

Software

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