9HRD | pdb_00009hrd

Crystal structure of the Class V GTP aptamer in complex with GTP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	291	methylpentanediol, potasium chloride, manganese chloride, spermine, cacodylate

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.268	α = 90
b = 127.216	β = 90.455
c = 68.368	γ = 90

Symmetry
Space Group	P 1 21 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	DECTRIS EIGER X 16M		2023-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	1.892	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.5	20.001	97.32	0.0897	0.0374	11.23	6.8		30103

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59			0.877	0.75

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	SAD	FREE R-VALUE	2.5	20.001	30100	1530	97.317	0.202	0.2003	0.2009	0.2378	0.2397	79.848

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]
0.544		0.297	-1.656		1.108

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	10.524
r_lrange_other	10.518
r_scangle_it	8.348
r_scangle_other	8.348
r_scbond_it	5.718
r_scbond_other	5.718
r_angle_refined_deg	1.873
r_angle_other_deg	0.531
r_dihedral_angle_other_2_deg	0.401
r_nbd_refined	0.396
r_symmetry_xyhbond_nbd_refined	0.302
r_nbtor_refined	0.245
r_xyhbond_nbd_refined	0.243
r_nbd_other	0.23
r_symmetry_nbd_other	0.21
r_symmetry_nbd_refined	0.139
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.068
r_ncsr_local_group_6	0.049
r_ncsr_local_group_1	0.045
r_ncsr_local_group_3	0.042
r_ncsr_local_group_4	0.038
r_ncsr_local_group_5	0.038
r_ncsr_local_group_2	0.037
r_metal_ion_refined	0.019
r_gen_planes_refined	0.013
r_bond_refined_d	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	5752
Solvent Atoms	74
Heterogen Atoms	276

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
Coot	model building
PHASER	phasing
Aimless	data scaling
pointless	data scaling
XDS	data reduction