8PAF | pdb_00008paf

Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[N-(3-Indolepropionic acid)sulfamoyl] 2-aminoethenoadenosine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YQM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	281	14% w/v PEG4000, 0.1 M sodium cacodylate pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.192	α = 90
b = 46.55	β = 94.844
c = 64.105	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		2022-09-26	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	2.1	18.486	99.8	0.082	0.091	0.039	0.998	14.9	5.3		13742			10.3

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	2.1	2.16	99.9		0.229	0.254	0.108	0.963		5.4

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	THROUGHOUT	2.1	18.486	13733	592	99.717	0.138	0.1357	0.15	0.1874	0.2	13.863

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]
1.983		-0.198	-0.522		-1.407

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.096
r_dihedral_angle_3_deg	14.259
r_dihedral_angle_2_deg	7.371
r_dihedral_angle_1_deg	6.852
r_lrange_it	5.041
r_lrange_other	4.787
r_scangle_it	2.902
r_scangle_other	2.901
r_mcangle_it	1.866
r_mcangle_other	1.866
r_scbond_it	1.788
r_scbond_other	1.787
r_angle_refined_deg	1.461
r_mcbond_it	1.228
r_mcbond_other	1.227
r_angle_other_deg	0.495
r_symmetry_xyhbond_nbd_refined	0.237
r_nbd_refined	0.235
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.171
r_nbd_other	0.147
r_symmetry_nbd_refined	0.146
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.081
r_symmetry_xyhbond_nbd_other	0.049
r_dihedral_angle_other_2_deg	0.021
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1762
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	39

Software

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