8X23 | pdb_00008x23

The Crystal Structure of MAPK13 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4YNO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	50mM (NH4)2 tartrate, 18% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.402	α = 90
b = 69.113	β = 90
c = 92.83	γ = 90

Symmetry
Space Group	P 21 21 21

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 9M		2023-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95371	CLSI	08ID-1

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	1.5	38.56	98.2	0.072	20	13.8		62675

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	1.5	1.54			0.833

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	1.5	38.56	62624	3164	97.976	0.126	0.1239	0.12	0.171	0.17	21.967

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]
-1.208			2.912		-1.703

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.994
r_dihedral_angle_3_deg	13.536
r_dihedral_angle_2_deg	6.678
r_dihedral_angle_1_deg	5.778
r_rigid_bond_restr	5.569
r_lrange_it	5.338
r_lrange_other	4.668
r_scangle_it	4.614
r_scangle_other	4.613
r_scbond_it	3.874
r_scbond_other	3.874
r_mcangle_other	3.748
r_mcangle_it	3.743
r_mcbond_it	3.495
r_mcbond_other	3.492
r_angle_refined_deg	1.437
r_angle_other_deg	0.52
r_symmetry_xyhbond_nbd_refined	0.222
r_nbd_refined	0.216
r_symmetry_nbd_refined	0.199
r_nbd_other	0.195
r_symmetry_nbd_other	0.188
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.185
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2803
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	24

Software

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