25WN | pdb_000025wn

Crystal structure of Candida albicans Eukaryotic translation initiation factor 5A

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	295	5% PEG 3350, 200mM sodium formiate, 10% glycerol, 50mM MES pH 6

Crystal Properties
Matthews coefficient	Solvent content
13.83	91.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.253	α = 90
b = 35.149	β = 92.997
c = 337.128	γ = 90

Symmetry
Space Group	P 1 21 1

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	RIGAKU HyPix-6000HE		2026-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU PhotonJet-S	1.54184

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	2.6	19.39	96	0.288	0.388	0.259	0.91	4.6	3.1		24965

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)
	2.6	2.72	95.6		1.345	1.798	1.185	0.277	1.3	3.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.6	19.39	24958	1296	95.361	0.334	0.333	0.333	0.3484	0.3484	RANDOM	27.644

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]
10.596		0.31	-22.54		11.944

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.485
r_dihedral_angle_3_deg	22.497
r_lrange_it	15.956
r_dihedral_angle_6_deg	13.748
r_dihedral_angle_1_deg	10.473
r_mcangle_it	9.694
r_scangle_it	9.098
r_mcbond_it	6.533
r_scbond_it	6.304
r_angle_refined_deg	3.102
r_symmetry_nbd_refined	0.381
r_symmetry_xyhbond_nbd_refined	0.375
r_nbtor_refined	0.261
r_chiral_restr	0.199
r_nbd_refined	0.191
r_xyhbond_nbd_refined	0.149
r_bond_refined_d	0.017
r_gen_planes_refined	0.013
r_ext_dist_refined_b	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1054
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
Aimless	data scaling
gemmi	data extraction
REFMAC	refinement
gemmi	data extraction
PHASER	phasing