9OWB | pdb_00009owb

Human WRN helicase in complex with allosteric ligand Compound 6

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, SITTING DROP		277	20.0% w/v PEG3350, 200 mM ammonium tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.085	α = 90.03
b = 58.394	β = 90
c = 131.907	γ = 90

Symmetry
Space Group	P 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 EIGER2 X 16M		2023-09-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	SLS	X10SA

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	1.556	53.5	94.4	0.036	0.998	11.4	2.3		234986

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	1.556	1.583	66.6		0.496	0.734	1.3	2.1

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	1.56	53.46	226751	8235	94.41	0.15124	0.1497	0.1603	0.19234	0.1972	RANDOM	31.791

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]
1.78	0.01	-0.03		0.45	-1.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.246
r_dihedral_angle_4_deg	15.39
r_dihedral_angle_3_deg	12.189
r_dihedral_angle_1_deg	6.443
r_long_range_B_refined	4.028
r_long_range_B_other	3.806
r_scangle_other	2.986
r_mcangle_it	2.869
r_mcangle_other	2.869
r_rigid_bond_restr	2.443
r_scbond_it	2.381
r_scbond_other	2.381
r_mcbond_it	2.198
r_mcbond_other	2.196
r_angle_refined_deg	1.331
r_angle_other_deg	1.304
r_chiral_restr	0.066
r_bond_other_d	0.009
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
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	13643
Nucleic Acid Atoms
Solvent Atoms	1504
Heterogen Atoms	297

Software

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