8PA9

Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl N2-methyl-2-aminoethenoadenosine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	281	12% w/v PEG4000, 0.1 M sodium cacodylate pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.597	α = 90
b = 46.314	β = 94.707
c = 64.01	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	PIXEL	RIGAKU HyPix-6000HE		2023-02-09	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	1.5	18.451	99.8	0.062	0.068	0.028	0.999	14.2	5.1		36820			9

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	1.5	1.53	98.9		0.503	0.598	0.315	0.84	2.3	2.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.5	18.451	36815	1878	99.702	0.151	0.149	0.1794	11.513

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]
1.353		-0.171	-0.48		-0.834

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.715
r_dihedral_angle_3_deg	14.721
r_dihedral_angle_2_deg	12.742
r_dihedral_angle_1_deg	6.14
r_lrange_it	5.051
r_lrange_other	4.721
r_scangle_it	2.881
r_scangle_other	2.88
r_mcangle_it	1.934
r_mcangle_other	1.933
r_scbond_it	1.877
r_scbond_other	1.877
r_angle_refined_deg	1.657
r_mcbond_it	1.213
r_mcbond_other	1.21
r_angle_other_deg	0.606
r_symmetry_nbd_refined	0.264
r_nbd_refined	0.232
r_symmetry_nbd_other	0.201
r_symmetry_xyhbond_nbd_refined	0.2
r_xyhbond_nbd_refined	0.195
r_nbtor_refined	0.177
r_nbd_other	0.156
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1762
Nucleic Acid Atoms
Solvent Atoms	332
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing