9HRC | pdb_00009hrc

Structure of MNK2 in complex with inhibitor NUCC-0201049

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Unpublished structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	298	0.02 M Magnesium Chloride, 0.1 M HEPES-NaOH pH 7.1 and 29% w/v Sodium Polyacrylate 5100

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.927	α = 90
b = 106.927	β = 90
c = 69.952	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 EIGER X 16M		2020-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.976254	MAX IV	BioMAX

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	3.16	55.82	100	0.143	0.15	0.045	0.999	15.2	20.3		8187			77.3

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	3.16	3.38	100		1.183	1.241	0.374	0.864	2.8	20.9

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	FOURIER SYNTHESIS	FREE R-VALUE	3.161	35.002	8166	383	99.902	0.186	0.1831	0.1927	0.2434	0.2574	99.436

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]
-3.735	-1.868		-3.735		12.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.865
r_dihedral_angle_6_deg	12.102
r_lrange_it	12.076
r_lrange_other	12.074
r_mcangle_it	7.541
r_mcangle_other	7.539
r_scangle_it	7.25
r_scangle_other	7.248
r_dihedral_angle_1_deg	5.736
r_dihedral_angle_2_deg	4.571
r_dihedral_angle_other_3_deg	4.539
r_mcbond_it	4.474
r_mcbond_other	4.47
r_scbond_it	4.266
r_scbond_other	4.264
r_angle_refined_deg	0.768
r_angle_other_deg	0.27
r_nbd_refined	0.2
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.149
r_nbd_other	0.119
r_symmetry_xyhbond_nbd_refined	0.108
r_symmetry_nbd_refined	0.101
r_symmetry_xyhbond_nbd_other	0.097
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.038
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2249
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms	29

Software

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