9P51 | pdb_00009p51

Crystal structure of MLH1-CTD with CHDI-00915848

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9P4B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	25% PEG 8K, 200 mM sodium acetate, 85 mM sodium cacodylate pH 6.5 and 12% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.06	α = 90
b = 225.57	β = 90
c = 44.09	γ = 90

Symmetry
Space Group	P 21 21 2

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		2023-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.033167	APS	23-ID-B

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	2.25	36	99.9	0.114	0.048	0.999	9.8	6.6		29972

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	2.25	2.31	100		2.302	0.933	0.345	0.8

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	2.25	35.745	29909	1548	99.876	0.2	0.1993	0.2046	0.2187	0.2212	60.756

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]
-1.1			-2.34		3.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.029
r_dihedral_angle_6_deg	13.952
r_dihedral_angle_1_deg	6.267
r_lrange_it	5.847
r_lrange_other	5.846
r_dihedral_angle_2_deg	5.356
r_scangle_it	3.922
r_scangle_other	3.922
r_mcangle_it	3.253
r_mcangle_other	3.252
r_scbond_it	2.288
r_scbond_other	2.287
r_mcbond_it	1.961
r_mcbond_other	1.959
r_angle_refined_deg	0.924
r_angle_other_deg	0.312
r_nbd_refined	0.205
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.178
r_nbd_other	0.176
r_xyhbond_nbd_refined	0.143
r_symmetry_nbd_refined	0.128
r_symmetry_xyhbond_nbd_refined	0.093
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.044
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4171
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing