9QBV | pdb_00009qbv

Crystal structure of WRN in complex with (R)-11 (GSK4766470)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YHR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	10% PEG 6000, 0.1 M HEPES pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.184	α = 90
b = 58.31	β = 90
c = 132.998	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 EIGER X 16M		2022-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.15	50	89.9	0.088	0.1	0.046	0.983	12.7	4.4		23142

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	85.3		0.646	0.718	0.306	0.821	2.3	4.5

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	2.15	39.34	21940	1156	89.84	0.19636	0.19301	0.2035	0.25839	0.2625	RANDOM	45.933

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]
1.34			-0.66		-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.293
r_dihedral_angle_2_deg	9.809
r_long_range_B_refined	9.376
r_long_range_B_other	9.374
r_dihedral_angle_1_deg	8.294
r_scangle_other	7.425
r_mcangle_it	5.57
r_mcangle_other	5.569
r_scbond_it	5.003
r_scbond_other	5.002
r_mcbond_it	3.98
r_mcbond_other	3.979
r_angle_refined_deg	1.195
r_angle_other_deg	0.391
r_chiral_restr	0.058
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3330
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing