8OQC

Dirhodium tetraacetate/ribonuclease A adduct in the P3221 space group (1 h soaking)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5OGH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	293	2.5 M NaCl 3.3 M HCOONa 0.1 M Acetate buffer

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.129	α = 90
b = 67.129	β = 90
c = 64.979	γ = 120

Symmetry
Space Group	P 32 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	93	PIXEL	RIGAKU HyPix-6000HE		2022-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU PhotonJet-R	1.5406

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.5	21.97	100	0.074	0.022	0.999	22.6	11.1		27554

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	100		2.144	0.875	0.325	0.9

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	FREE R-VALUE	1.5	21.97	27520	1379	99.949	0.182	0.1804	0.2151	20.74

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]
-0.001			-0.001		0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.111
r_dihedral_angle_3_deg	14.932
r_dihedral_angle_2_deg	8.411
r_lrange_it	6.995
r_dihedral_angle_1_deg	6.734
r_lrange_other	6.541
r_scangle_other	5.007
r_scangle_it	4.916
r_mcangle_it	3.433
r_mcangle_other	3.431
r_angle_refined_deg	3.227
r_scbond_other	3.221
r_scbond_it	3.177
r_mcbond_it	2.3
r_mcbond_other	2.298
r_angle_other_deg	0.599
r_xyhbond_nbd_refined	0.3
r_nbd_refined	0.235
r_symmetry_xyhbond_nbd_refined	0.233
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.18
r_nbd_other	0.162
r_symmetry_nbd_refined	0.136
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.087
r_symmetry_xyhbond_nbd_other	0.029
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	951
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	39

Software

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