9P4B | pdb_00009p4b

Crystal structure of MLH1-CTD with peptide QAVLSRFFQ

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	11% PEG 20K , 100 mM MES pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.92	α = 90
b = 70.92	β = 90
c = 273.79	γ = 90

Symmetry
Space Group	P 41 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 PILATUS 6M		2020-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.0332	APS	23-ID-D

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	2.44	50	99.7	0.12	0.126	0.036	0.998	14.4	12.3		27046

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	2.44	2.5	96.9		1.906	2.007	0.612	0.42	1.1	10.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4X7J	2.44	49.25	25657	1321	99.53	0.208	0.2056	0.2087	0.249	0.2498	Random selection	62.108

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]
-1.689			-1.689		3.377

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.484
r_dihedral_angle_6_deg	13.36
r_lrange_other	7.002
r_lrange_it	7.001
r_dihedral_angle_2_deg	6.893
r_dihedral_angle_1_deg	6.524
r_scangle_it	4.879
r_scangle_other	4.878
r_mcangle_it	4.273
r_mcangle_other	4.272
r_scbond_it	2.931
r_scbond_other	2.931
r_mcbond_it	2.629
r_mcbond_other	2.628
r_angle_refined_deg	1.252
r_angle_other_deg	0.437
r_nbd_refined	0.217
r_symmetry_nbd_refined	0.199
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.146
r_nbd_other	0.146
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.062
r_chiral_restr_other	0.017
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4254
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms

Software

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