8P9B

Crystal Structure of Mnk2-D228G in complex with Tinodasertib

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HW7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	292	24% (w/v) polyacrylic acid 5100, 2% (v/v) 2-Methyl-2,4-pentanediol, 100mM HEPES, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.79	67.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.91	α = 90
b = 105.91	β = 90
c = 71.5	γ = 120

Symmetry
Space Group	P 32 2 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 PILATUS 6M		2019-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.59	56.39	99.9	0.05	1	24.4	9.6		14740

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.59	2.66	100		1.617	0.558	1.2	8.1

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.59	50.005	14721	738	99.932	0.211	0.2081	0.2636	88.708

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]
0.11	0.055		0.11		-0.357

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.464
r_dihedral_angle_6_deg	15.095
r_dihedral_angle_other_3_deg	11.264
r_lrange_it	9.667
r_lrange_other	9.665
r_scangle_it	8.579
r_scangle_other	8.576
r_dihedral_angle_1_deg	7.074
r_dihedral_angle_2_deg	6.976
r_mcangle_it	6.728
r_mcangle_other	6.725
r_scbond_it	6.245
r_scbond_other	6.242
r_mcbond_it	4.709
r_mcbond_other	4.707
r_angle_refined_deg	1.358
r_chiral_restr_other	1.188
r_angle_other_deg	0.542
r_symmetry_nbd_refined	0.251
r_nbd_refined	0.228
r_symmetry_nbd_other	0.193
r_nbd_other	0.188
r_nbtor_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.161
r_xyhbond_nbd_refined	0.124
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2015
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing