9MK1 | pdb_00009mk1

Crystal structure of WRN helicase with bound compound 6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9MJT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	24.5% w/v PEG1500, 0.1 M MMT, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.82	α = 90
b = 57.75	β = 90
c = 133.53	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	95	PIXEL	DECTRIS EIGER2 X CdTe 16M		2023-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.88560	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.12	53.06	99.4	0.094	0.997	12.1	7.3		26085

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	2.12	2.15			0.564		6.6

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	2.12	53.06	24831	1252	99.36	0.22987	0.22801	0.2302	0.26659	0.2659	RANDOM	47.055

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]
-1.21			0.93		0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.952
r_dihedral_angle_4_deg	16.057
r_dihedral_angle_3_deg	13.644
r_dihedral_angle_1_deg	6.716
r_long_range_B_refined	5.106
r_long_range_B_other	5.1
r_mcangle_it	3.265
r_mcangle_other	3.265
r_scangle_other	2.84
r_mcbond_it	1.951
r_mcbond_other	1.95
r_scbond_it	1.703
r_scbond_other	1.702
r_angle_refined_deg	1.348
r_angle_other_deg	1.118
r_chiral_restr	0.055
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3368
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	49

Software

Software
Software Name	Purpose
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
XSCALE	data scaling
REFMAC	refinement