8XX1 | pdb_00008xx1

The Crystal Structure of MAPKAP kinase 2 domain from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3M42

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.1M Sodium malonate dibasic monohydrate, 0.1M HEPES pH 7, 0.5% v/v Jeffamine ED2003

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.239	α = 90
b = 103.239	β = 90
c = 166.788	γ = 120

Symmetry
Space Group	P 63 2 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		2023-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953732	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.55	49.31	100	0.998	18.2	21.5		17831

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.66			0.9	4.7

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	2.55	49.31	17799	862	100	0.17	0.1661	0.17	0.2454	0.25	35.866

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]
-0.464	-0.232		-0.464		1.504

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.472
r_dihedral_angle_6_deg	15.801
r_lrange_it	10.091
r_lrange_other	10.072
r_dihedral_angle_1_deg	7.368
r_scangle_it	7.349
r_scangle_other	7.347
r_mcangle_it	6.209
r_mcangle_other	6.209
r_dihedral_angle_2_deg	6.191
r_scbond_it	4.504
r_scbond_other	4.502
r_mcbond_it	3.976
r_mcbond_other	3.966
r_angle_refined_deg	1.622
r_angle_other_deg	0.532
r_nbd_other	0.25
r_nbd_refined	0.218
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.177
r_symmetry_xyhbond_nbd_refined	0.133
r_symmetry_nbd_refined	0.116
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2383
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms

Software

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