7CBX

Crystal structure of MAP2K7 complexed with a covalent inhibitor 12

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5Y90

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.965	α = 90
b = 70.517	β = 90
c = 84.346	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	95	PIXEL	DECTRIS EIGER X 16M		2019-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

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	2.06	50	99.8	0.062	17.4	6.5		23058

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	2.06	2.19			0.47

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5y90	2.061	46.162	23058	1245	99.801	0.184	0.1816	0.2236	40.38

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]
1.176			-1.318		0.142

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.19
r_dihedral_angle_4_deg	24.242
r_dihedral_angle_3_deg	16.02
r_lrange_it	10.343
r_lrange_other	10.342
r_scangle_it	7.769
r_scangle_other	7.767
r_dihedral_angle_1_deg	6.948
r_mcangle_it	5.646
r_mcangle_other	5.645
r_scbond_it	5.195
r_scbond_other	5.195
r_mcbond_it	3.857
r_mcbond_other	3.856
r_angle_refined_deg	1.696
r_angle_other_deg	1.36
r_symmetry_nbd_refined	0.259
r_nbd_refined	0.226
r_nbd_other	0.192
r_symmetry_nbd_other	0.19
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.146
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.08
r_symmetry_xyhbond_nbd_other	0.036
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2244
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing