9GYS | pdb_00009gys

X-ray structure of the adduct formed upon reaction of RNase A with [Ru2(D-p-FPhF)(O2CCH3)2(O2CO)] complex

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	22% PEG4K, 10 mM sodium citrate buffer at pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.54	α = 90
b = 32.6	β = 90.014
c = 72.35	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	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	1.74	50.27	94.4	0.052	0.997	11.6	2.9		23214

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	1.74	1.77			0.466	0.745	2.1

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.74	50.27	22932	1160	93.486	0.195	0.1922	0.1992	0.26	0.2625	0.261	25.606

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]
-0.082		0.147	0.084		-0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.896
r_dihedral_angle_3_deg	11.689
r_lrange_it	7.35
r_lrange_other	7.122
r_dihedral_angle_1_deg	7.117
r_dihedral_angle_2_deg	5.718
r_scangle_it	4.56
r_scangle_other	4.557
r_mcangle_it	4.003
r_mcangle_other	4.002
r_scbond_it	2.933
r_scbond_other	2.827
r_mcbond_it	2.641
r_mcbond_other	2.641
r_angle_refined_deg	1.581
r_angle_other_deg	0.552
r_symmetry_xyhbond_nbd_refined	0.216
r_symmetry_nbd_other	0.204
r_symmetry_nbd_refined	0.197
r_nbd_refined	0.191
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.173
r_nbd_other	0.17
r_xyhbond_nbd_other	0.125
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.077
r_gen_planes_refined	0.008
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1898
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	78

Software

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