36HB | pdb_000036hb

Crystal Structure of De Novo Protein Inhibitor of eEF2K

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, HANGING DROP	6	293	60 % tacsimate

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.97	α = 90
b = 86.97	β = 90
c = 221.58	γ = 120

Symmetry
Space Group	P 65 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 EIGER2 X 16M		2025-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

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	2.49	44.63	99.5	0.83	14.7	4.1		18127

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	2.492	44.625	18127	882	99.972	0.202	0.1988	0.1988	0.2759	0.2762	48.021

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]
0.225	0.112		0.225		-0.729

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	30.523
r_lrange_it	30.52
r_scangle_it	29.474
r_scangle_other	29.468
r_scbond_it	22.207
r_scbond_other	22.201
r_mcangle_it	20.857
r_mcangle_other	20.854
r_dihedral_angle_3_deg	20.519
r_dihedral_angle_2_deg	17.506
r_mcbond_it	16.509
r_mcbond_other	16.49
r_dihedral_angle_6_deg	15.859
r_dihedral_angle_1_deg	9.184
r_angle_refined_deg	3.99
r_angle_other_deg	1.409
r_symmetry_nbd_refined	0.356
r_xyhbond_nbd_refined	0.307
r_symmetry_xyhbond_nbd_refined	0.262
r_nbd_refined	0.26
r_nbd_other	0.228
r_chiral_restr	0.211
r_nbtor_refined	0.189
r_symmetry_nbd_other	0.18
r_symmetry_xyhbond_nbd_other	0.142
r_symmetry_nbtor_other	0.102
r_metal_ion_refined	0.059
r_bond_refined_d	0.027
r_gen_planes_refined	0.016
r_ext_dist_refined_b	0.004
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3012
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	18

Software

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