9H7S | pdb_00009h7s

MITF in complex with 1-(3-chlorophenyl)-6-((1-hydroxycyclohexyl)ethynyl)-1H-indole-2-carboxylic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		undisclosed in-house structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.2 M ammonium sulfate, 5 % (v/v) PEG 400, 0.1 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.156	α = 90
b = 90.156	β = 90
c = 82.833	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 EIGER X 16M		2021-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0000290	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.986	50.52	94.9	0.013	1	27.9	19.6		22926			45.01

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.986	2.02			0.352	0.81	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.99	50.52	1.36	22914	1090	94.82	0.2027	0.2008	0.2002	0.2445	0.2444	55.9

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.2159
f_angle_d	0.9286
f_chiral_restr	0.0515
f_bond_d	0.0097
f_plane_restr	0.0089

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1558
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	67

Software

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