8PA6

Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl 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
2.11	41.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.845	α = 90
b = 46.324	β = 94.799
c = 63.971	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		2022-09-23	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	1.58	19.101	99.9	0.074	0.082	0.035	0.998	15.3	5.4		31671			8.2

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	1.58	1.61	100		0.661	0.775	0.396	0.742	2.1	3.6

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	1.58	19.101	31671	1625	99.912	0.15	0.1474	0.1913	10.824

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]
1.397		-0.114	-0.473		-0.893

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.953
r_dihedral_angle_3_deg	14.214
r_dihedral_angle_2_deg	7.088
r_dihedral_angle_1_deg	6.217
r_lrange_it	5.488
r_lrange_other	4.783
r_scangle_it	2.558
r_scangle_other	2.558
r_mcangle_it	1.705
r_mcangle_other	1.704
r_scbond_it	1.656
r_scbond_other	1.656
r_angle_refined_deg	1.54
r_mcbond_it	1.091
r_mcbond_other	1.09
r_angle_other_deg	0.547
r_nbd_refined	0.244
r_symmetry_nbd_other	0.202
r_xyhbond_nbd_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.183
r_nbtor_refined	0.175
r_symmetry_nbd_refined	0.162
r_dihedral_angle_other_2_deg	0.143
r_nbd_other	0.138
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.01
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	1766
Nucleic Acid Atoms
Solvent Atoms	390
Heterogen Atoms	36

Software

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