9GYP | pdb_00009gyp

Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with KV24

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
2.08	40.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.957	α = 90
b = 46.446	β = 94.533
c = 63.788	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		2023-12-14	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	1.8	18.416	99.3	0.056	0.065	0.032	0.998	15.1	3.8		21094			12.3

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	1.8	1.84	98.7		0.344	0.428	0.251	0.874	2.9	2.4

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	1.801	18.416	21069	981	99.144	0.143	0.141	0.1555	0.1908	0.2033	15.055

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]
1.808		-0.363	-0.344		-1.389

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.315
r_dihedral_angle_3_deg	13.013
r_dihedral_angle_2_deg	7.627
r_dihedral_angle_1_deg	6.518
r_lrange_it	5.346
r_lrange_other	5.105
r_scangle_it	3.254
r_scangle_other	3.182
r_scbond_it	2.31
r_scbond_other	2.005
r_mcangle_it	1.98
r_mcangle_other	1.98
r_angle_refined_deg	1.651
r_mcbond_it	1.29
r_mcbond_other	1.289
r_angle_other_deg	0.587
r_nbd_refined	0.218
r_symmetry_nbd_other	0.199
r_symmetry_xyhbond_nbd_refined	0.199
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.172
r_nbd_other	0.158
r_symmetry_nbd_refined	0.115
r_symmetry_xyhbond_nbd_other	0.114
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1762
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	33

Software

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