8R5V

Crystal structure of bovine pancreatic ribonuclease A in complex with [Sp-PS]-mU-dT dinucleotide

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	281	22-25 % (w/v) PEG 4000, 20 mM sodium citrate pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.315	α = 90
b = 32.709	β = 90.069
c = 72.802	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		2023-07-14	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	17.435	98.8	0.078	0.094	0.051	0.994	9.6	3.1		22015			9.4

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	95.8		0.243	0.294	0.161	0.93	3.4	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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	17.435	21996	1122	98.517	0.167	0.1641	0.2303	15.904

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]
0.162		0.168	0.075		-0.237

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.987
r_dihedral_angle_3_deg	13.084
r_dihedral_angle_1_deg	6.906
r_lrange_it	6.697
r_lrange_other	6.345
r_dihedral_angle_2_deg	5.82
r_scangle_it	4.053
r_scangle_other	4.052
r_mcangle_it	2.759
r_mcangle_other	2.759
r_scbond_it	2.387
r_scbond_other	2.384
r_mcbond_it	1.713
r_mcbond_other	1.704
r_angle_refined_deg	1.548
r_angle_other_deg	0.562
r_xyhbond_nbd_refined	0.283
r_nbd_refined	0.219
r_symmetry_nbd_other	0.203
r_nbd_other	0.187
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.154
r_symmetry_nbd_refined	0.091
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.078
r_symmetry_xyhbond_nbd_other	0.036
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1875
Nucleic Acid Atoms
Solvent Atoms	383
Heterogen Atoms	48

Software

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