8XFM | pdb_00008xfm

The Crystal Structure of MNK2 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AC3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M NH4Ac, 0.1M Bis-Tris pH5.5, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.859	α = 90
b = 103.859	β = 90
c = 73.29	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		2021-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.6	45.013	100	0.081	27.5	14.6		14349

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.72			0.87	3.5

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	MOLECULAR REPLACEMENT	FREE R-VALUE	2.6	45.013	14349	645	99.951	0.193	0.1901	0.2	0.2536	0.26	62.713

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]
-1.031	-0.516		-1.031		3.346

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.536
r_dihedral_angle_3_deg	12.909
r_lrange_other	11.349
r_lrange_it	11.348
r_scangle_it	7.843
r_scangle_other	7.841
r_mcangle_it	7.743
r_mcangle_other	7.74
r_dihedral_angle_1_deg	6.201
r_dihedral_angle_2_deg	5.631
r_scbond_it	4.865
r_scbond_other	4.864
r_mcbond_it	4.775
r_mcbond_other	4.764
r_dihedral_angle_other_3_deg	4.687
r_angle_refined_deg	1.226
r_angle_other_deg	0.415
r_symmetry_xyhbond_nbd_refined	0.267
r_nbd_refined	0.204
r_symmetry_nbd_refined	0.194
r_symmetry_nbd_other	0.189
r_nbd_other	0.185
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.069
r_chiral_restr	0.056
r_gen_planes_refined	0.005
r_bond_refined_d	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	2199
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	30

Software

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