9P40 | pdb_00009p40

MEKK1 SWIM and RING Domains

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.2	291.15	0.04 M NaH2PO4 and 0.96 M K2HPO4

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.832	α = 90
b = 119.832	β = 90
c = 56.581	γ = 120

Symmetry
Space Group	P 65

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		2022-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	2.95	41.171	99	0.203	0.222	0.091	0.99	7.5	5.8		8923			52.52

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	3.05	3.26	99.3		1.048	1.151	0.469	0.71	1.7	5.8

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	3.05	41.171	8920	450	98.935	0.181	0.1788	0.1795	0.2203	0.2209	70.69

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]
0.067	0.033		0.067		-0.216

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	34.394
r_lrange_it	34.393
r_scangle_it	20.62
r_scangle_other	20.615
r_mcangle_other	18.368
r_mcangle_it	18.354
r_dihedral_angle_3_deg	17.117
r_dihedral_angle_6_deg	15.496
r_dihedral_angle_2_deg	14.062
r_scbond_other	13.552
r_scbond_it	13.469
r_mcbond_other	11.748
r_mcbond_it	11.729
r_dihedral_angle_1_deg	6.765
r_rigid_bond_restr	5.468
r_angle_refined_deg	2.173
r_angle_other_deg	0.544
r_nbd_other	0.254
r_nbd_refined	0.225
r_symmetry_nbd_other	0.215
r_symmetry_nbd_refined	0.195
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.175
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_refined	0.046
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2735
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	6

Software

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