8P8P | pdb_00008p8p

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

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	10% w/v PEG4000, 0.1 M sodium cacodylate pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.725	α = 90
b = 46.552	β = 94.738
c = 64.101	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		2023-02-07	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	1.9	19.22	99.6	0.1	0.116	0.057	0.994	8.9	3.9		18317			10.9

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	1.9	1.94	98.7		0.331	0.4	0.22	0.891	2.5	2.9

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	1.9	19.22	18298	910	99.381	0.156	0.1544	0.17	0.19	0.2	14.134

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]
1.89		-0.4	-0.491		-1.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.604
r_dihedral_angle_3_deg	14.792
r_dihedral_angle_1_deg	6.422
r_dihedral_angle_2_deg	5.238
r_lrange_it	4.735
r_lrange_other	4.487
r_scangle_it	3.08
r_scangle_other	3.079
r_mcangle_it	1.964
r_mcangle_other	1.964
r_scbond_it	1.883
r_scbond_other	1.882
r_angle_refined_deg	1.461
r_mcbond_it	1.272
r_mcbond_other	1.27
r_angle_other_deg	0.505
r_nbd_refined	0.241
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.159
r_nbd_other	0.136
r_symmetry_nbd_refined	0.094
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1762
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	35

Software

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