8R7E | pdb_00008r7e

MutSbeta bound to compound CHDI-00898647 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 6.5; 0.2 M NH4 Acetate; 20-25 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.473	α = 109.331
b = 104.096	β = 91.808
c = 122.016	γ = 109.505

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		2022-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.783	113.659	92	0.071	0.062	0.98	9	2.3		79309

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.783	3.008	57.7		0.888	0.643	0.353	1.5	2.8

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	2.783	113.659	79308	3915	72.825	0.225	0.2226	0.2242	0.2657	0.2651	60.459

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]
-0.266	-0.193	0.096	-0.035	-0.067	0.356

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.004
r_dihedral_angle_4_deg	15.213
r_dihedral_angle_3_deg	14.546
r_dihedral_angle_6_deg	12.934
r_lrange_it	6.384
r_lrange_other	6.383
r_dihedral_angle_1_deg	6.241
r_dihedral_angle_other_3_deg	6.018
r_mcangle_it	4.053
r_mcangle_other	4.053
r_scangle_it	3.434
r_scangle_other	3.434
r_mcbond_it	2.352
r_mcbond_other	2.352
r_scbond_it	1.95
r_scbond_other	1.95
r_angle_refined_deg	1.297
r_angle_other_deg	1.112
r_nbtor_refined	0.148
r_nbd_refined	0.146
r_symmetry_xyhbond_nbd_refined	0.144
r_symmetry_nbd_other	0.142
r_nbd_other	0.138
r_symmetry_nbd_refined	0.125
r_xyhbond_nbd_refined	0.099
r_ext_dist_refined_d	0.073
r_symmetry_nbtor_other	0.072
r_symmetry_xyhbond_nbd_other	0.052
r_chiral_restr	0.047
r_ncsr_local_group_3	0.041
r_ncsr_local_group_4	0.037
r_ncsr_local_group_1	0.035
r_ncsr_local_group_2	0.03
r_bond_refined_d	0.003
r_gen_planes_refined	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	26824
Nucleic Acid Atoms	1819
Solvent Atoms	117
Heterogen Atoms	176

Software

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