8UB1

Structure of Butyl-5'-O-adenosine phosphoramidate/RNase A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AFK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	291	25% PEG 3350, 20 MM SODIUM CITRATE PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Butyl-5'-O-adenosine phosphoramidate was soaked into the crystals using a stock solution of 100 mM, to achieve ~35 mM in the soaking solution.

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.027	α = 90
b = 32.123	β = 90.71
c = 72.425	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	Bruker PHOTON II		2023-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.3418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.53	19.57	99.5	0.089	11.74	8.2		35060

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.53	1.63	99.4		0.601	1.1	3.88

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.53	19.57	31580	1595	94.17	0.24773	0.2453	0.29675	RANDOM	23.26

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]
-0.76		-0.27	0.61		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.705
r_dihedral_angle_1_deg	7.038
r_long_range_B_refined	6.004
r_long_range_B_other	5.985
r_dihedral_angle_2_deg	5.742
r_scangle_other	4.035
r_mcangle_it	3.205
r_mcangle_other	3.204
r_scbond_it	2.547
r_scbond_other	2.546
r_mcbond_it	2.062
r_mcbond_other	2.036
r_angle_refined_deg	1.489
r_angle_other_deg	0.49
r_chiral_restr	0.066
r_gen_planes_refined	0.008
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1876
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
MOLREP	phasing