8R7C | pdb_00008r7c

MutSbeta bound to compound CHDI-00915542 in the canonical DNA-mismatch bound form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3THY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	0.1 MES pH 7.25; 0.2 M NH4 Acetate; 20- 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.222	α = 110.029
b = 104.789	β = 91.198
c = 121.263	γ = 110.501

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 EIGER X 16M		2022-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9999	SLS	X06SA

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	2.82	112.46	92.7	0.058	0.075	0.047	0.985	5.5	2.3		73299

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	2.82	3.12	59.5		0.514	0.66	0.406	0.701	1.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.82	112.46	73299	3646	70.106	0.203	0.2013	0.2048	0.2305	0.2343	66.779

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]
-0.228	-0.237	0.342	-0.072	-0.212	0.436

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.616
r_dihedral_angle_3_deg	15.252
r_dihedral_angle_4_deg	14.5
r_lrange_it	7.291
r_lrange_other	7.291
r_dihedral_angle_1_deg	6.538
r_mcangle_it	4.54
r_mcangle_other	4.54
r_scangle_it	4.184
r_scangle_other	4.184
r_mcbond_it	2.642
r_mcbond_other	2.642
r_scbond_it	2.372
r_scbond_other	2.372
r_angle_refined_deg	1.304
r_angle_other_deg	1.115
r_nbd_refined	0.148
r_nbtor_refined	0.148
r_nbd_other	0.146
r_symmetry_nbd_other	0.143
r_symmetry_nbd_refined	0.126
r_symmetry_xyhbond_nbd_refined	0.11
r_xyhbond_nbd_refined	0.096
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.048
r_ncsr_local_group_2	0.048
r_ncsr_local_group_3	0.047
r_ncsr_local_group_1	0.042
r_ncsr_local_group_4	0.022
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27707
Nucleic Acid Atoms	1802
Solvent Atoms	69
Heterogen Atoms	139

Software

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