9FYW | pdb_00009fyw

X-ray structure of the adduct formed upon reaction of RNase A with [Ru2Cl(D-p-CNPhF)(O2CCH3)3]

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.1	293	Free-interface diffusion of a 10 uL of 30 mg/ml protein solution, 20 mM sodium citrate at pH 5.3 agaist 10 ul isopropanol 99.9% isopropanol

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.62	α = 90
b = 32.74	β = 90.29
c = 72.25	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	DECTRIS PILATUS 6M		2022-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.4	72.25	91	0.048	0.999	19.4	5.6		36934

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.53			0.494	0.82	2.2

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	FREE R-VALUE	1.4	72.249	36934	1758	78.803	0.176	0.1745	0.1844	0.2143	0.2203	19.483

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

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.178
r_dihedral_angle_3_deg	11.478
r_lrange_it	8.439
r_lrange_other	8.383
r_dihedral_angle_1_deg	7.041
r_scangle_other	4.445
r_scangle_it	4.393
r_dihedral_angle_2_deg	4.073
r_mcangle_it	4.041
r_mcangle_other	4.039
r_scbond_other	2.802
r_scbond_it	2.792
r_mcbond_it	2.539
r_mcbond_other	2.539
r_angle_refined_deg	1.756
r_angle_other_deg	0.607
r_nbd_refined	0.212
r_symmetry_nbd_other	0.2
r_symmetry_nbd_refined	0.2
r_nbd_other	0.185
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.172
r_symmetry_xyhbond_nbd_other	0.159
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.084
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1894
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing