7ZMP | pdb_00007zmp

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-055

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	2.4M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
6.25	80.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.109	α = 90
b = 159.267	β = 90
c = 220.04	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	3.626	129.07	100	1	3.9	6.5		36355

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	3.63	3.69			0.2

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	3.626	129.017	36185	1808	99.59	0.334	0.3322	0.33	0.3594	0.36	125.931

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]
0.787			-0.234		-0.553

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.499
r_lrange_other	21.253
r_lrange_it	21.252
r_dihedral_angle_3_deg	17.312
r_mcangle_it	14.224
r_mcangle_other	14.223
r_dihedral_angle_4_deg	13.673
r_scangle_it	13.36
r_scangle_other	13.359
r_mcbond_other	8.708
r_mcbond_it	8.707
r_scbond_it	7.957
r_scbond_other	7.956
r_dihedral_angle_1_deg	6.971
r_angle_refined_deg	1.375
r_angle_other_deg	1.186
r_symmetry_xyhbond_nbd_refined	0.394
r_nbd_other	0.227
r_nbd_refined	0.221
r_symmetry_nbd_other	0.206
r_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.141
r_symmetry_nbtor_other	0.08
r_ncsr_local_group_2	0.066
r_ncsr_local_group_1	0.059
r_xyhbond_nbd_other	0.057
r_symmetry_xyhbond_nbd_other	0.054
r_chiral_restr	0.051
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8640
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms

Software

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