9R9M | pdb_00009r9m

Crystal Structure of human MLH1 C-terminal domain with cyclic peptide (2S)-N-[(6S,9S,12S,15S,18S,26aR)-12-(4-aminobutyl)-18-benzyl-21-(2-carbamoylethyl)-9-(hydroxymethyl)- 15-[(4-hydroxyphenyl)methyl]-1,7,10,13,16,19,22-heptaoxo-hexacosahydropyrrolo[2,1-c]1,4,7,10,13,16,19-heptaazacyclotetracosan-6-yl]-2-[(2S)-2-acetamidopropanamido]-3-methylbutanamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.25	293	14% PEG 8K 200 mM Ca-Acetate 100 mM MES pH 6.25

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.302	α = 90
b = 57.43	β = 90
c = 118.007	γ = 90

Symmetry
Space Group	P 21 21 21

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 X 16M		2023-06-14	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)	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	2.28	85.907	100	0.09	0.096	0.034	0.9946	10.905	8.4		39599

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	2.281	2.321	100		1.412	1.515	0.539	0.5268		8.03

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.281	85.907	39596	2748	99.952	0.197	0.1953	0.2	0.2202	0.2256	Random selection	57.337

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]
-0.315			1.968		-1.653

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_other_3_deg	26.76
r_dihedral_angle_other_6_deg	16.173
r_dihedral_angle_6_deg	13.785
r_dihedral_angle_3_deg	13.068
r_lrange_other	7.835
r_lrange_it	7.829
r_dihedral_angle_1_deg	6.324
r_scangle_it	5.876
r_scangle_other	5.875
r_mcangle_other	4.691
r_mcangle_it	4.69
r_scbond_it	3.632
r_scbond_other	3.631
r_mcbond_it	3.219
r_mcbond_other	3.215
r_angle_refined_deg	1.286
r_angle_other_deg	0.569
r_dihedral_angle_2_deg	0.342
r_nbd_refined	0.193
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.167
r_symmetry_nbd_other	0.166
r_nbd_other	0.162
r_xyhbond_nbd_refined	0.114
r_symmetry_xyhbond_nbd_refined	0.112
r_symmetry_nbtor_other	0.07
r_chiral_restr	0.067
r_symmetry_metal_ion_refined	0.062
r_ncsr_local_group_1	0.029
r_bond_other_d	0.005
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4075
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	132

Software

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