8RAZ | pdb_00008raz

The crystal structure of DNA-bound human MutSbeta (MSH2_E749A/MSH3_E976A) in the canonical mismatch bound conformation with ADP bound in MSH2 and MSH3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8RAU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.1 M MES pH 6.5 -7.5, 0.2 M Ammonium Acetate, 20 - 25 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.32	α = 67.13
b = 92.414	β = 86.69
c = 94.216	γ = 75.82

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 S 16M		2023-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000064	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.843	56.39	93.6	0.993	5	2.3		46613

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	2.843	2.892			0.403

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	2.843	56.39	45123	1253	93	0.21566	0.21389	0.2157	0.27928	0.282	RANDOM	59.273

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]
3.11	-1.6	1.39	-0.3	1.46	-1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.575
r_dihedral_angle_3_deg	14.613
r_dihedral_angle_4_deg	12.311
r_dihedral_angle_1_deg	6.479
r_long_range_B_refined	6.405
r_long_range_B_other	6.405
r_mcangle_it	4.168
r_mcangle_other	4.168
r_scangle_other	3.787
r_mcbond_it	2.442
r_mcbond_other	2.442
r_scbond_it	2.179
r_scbond_other	2.179
r_angle_refined_deg	1.315
r_angle_other_deg	1.133
r_chiral_restr	0.048
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.002
r_bond_other_d	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	13852
Nucleic Acid Atoms	780
Solvent Atoms	61
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing