9EIE | pdb_00009eie

Trypanosomatid-specific protein of unknown function

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AlphaFold3 run Oct 2024

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	0.1 M K2HPO4, 0.1 M Tris pH 8, 30% PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
2.84	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.225	α = 90
b = 71.647	β = 94.616
c = 67.084	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 210		2004-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	1.0	ALS	5.0.1

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	2.42	45.714	88.8	0.099	0.118	0.062	0.996	8.3	3.3		17796

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	2.42	2.51		40.3	0.482	0.629	0.398	0.702		1.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	AlphaFold3-generated model, from run in Oct 2024	2.45	45.714	17576	908	91.115	0.204	0.2025	0.2076	0.231	0.2291	43.325

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]
-0.34		-0.368	0.188		0.209

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.856
r_dihedral_angle_4_deg	26.192
r_dihedral_angle_3_deg	19.945
r_lrange_it	8.004
r_lrange_other	8
r_dihedral_angle_1_deg	7.929
r_scangle_it	5.379
r_scangle_other	5.377
r_mcangle_it	4.579
r_mcangle_other	4.578
r_scbond_it	3.175
r_scbond_other	3.174
r_mcbond_it	2.79
r_mcbond_other	2.786
r_angle_refined_deg	2.15
r_angle_other_deg	1.551
r_nbd_refined	0.241
r_symmetry_nbd_refined	0.22
r_symmetry_nbd_other	0.202
r_nbd_other	0.199
r_xyhbond_nbd_refined	0.198
r_metal_ion_refined	0.174
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.149
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.089
r_ncsr_local_group_1	0.082
r_gen_planes_other	0.02
r_bond_other_d	0.018
r_bond_refined_d	0.016
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2662
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	14

Software

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