9OWD | pdb_00009owd

Human WRN helicase in complex with allosteric ligand Compound 9

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		proprietary model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	23-24.5% w/v PEG1500, 100 mM MMT, pH 5.75-6.25

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.984	α = 90
b = 58.268	β = 90
c = 132.42	γ = 90

Symmetry
Space Group	P 21 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 EIGER2 XE 16M		2023-08-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.96	66.21	100	0.06	0.999	15.4	8.4		32828

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.964	1.998	100		1.472	0.545	1.3	8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.96	53.39	27816	2953	93.71	0.22973	0.22518	0.2291	0.27228	0.2749	RANDOM	48.046

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]
-0.39			0.26		0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.234
r_dihedral_angle_4_deg	15.222
r_dihedral_angle_3_deg	13.311
r_dihedral_angle_1_deg	6.59
r_long_range_B_refined	4.862
r_rigid_bond_restr	4.862
r_long_range_B_other	4.855
r_mcangle_it	3.076
r_mcangle_other	3.075
r_scangle_other	2.698
r_mcbond_it	1.843
r_mcbond_other	1.842
r_scbond_it	1.627
r_scbond_other	1.626
r_angle_refined_deg	1.331
r_angle_other_deg	1.192
r_chiral_restr	0.053
r_bond_other_d	0.009
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3325
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	74

Software

Software
Software Name	Purpose
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction