9MJS | pdb_00009mjs

Crystal structure of WRN helicase with bound AMPPNP

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	6	277	30% Jeffamine ED 2003, 0.2 M NaCl, 0.2 M NDSB-201, 0.1 M MES

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.202	α = 90
b = 93.737	β = 104.44
c = 53.782	γ = 90

Symmetry
Space Group	C 1 2 1

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 S 16M		2022-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00	SLS	X10SA

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	1.84	45.41	96.3	0.08	0.997	8.2	2.8		41646

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	1.84	1.87	96.2		0.528		2.9

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	1.84	45.41	39208	2413	96.17	0.19157	0.18946	0.1962	0.22518	0.228	RANDOM	32.904

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]
2.34		0.17	-1.81		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.696
r_dihedral_angle_4_deg	18.316
r_dihedral_angle_3_deg	12.52
r_dihedral_angle_1_deg	6.763
r_long_range_B_refined	5.207
r_long_range_B_other	5.156
r_scangle_other	3.575
r_mcangle_it	2.858
r_mcangle_other	2.858
r_scbond_it	2.258
r_scbond_other	2.258
r_mcbond_it	1.867
r_mcbond_other	1.862
r_angle_refined_deg	1.38
r_angle_other_deg	1.217
r_chiral_restr	0.066
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.001
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	3239
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	32

Software

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