7QQ0 | pdb_00007qq0

X-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] with RNase A (2)

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
2	VAPOR DIFFUSION, HANGING DROP	5.1	298	22% PEG 4K 10 mM sodium citrate buffer pH 5.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.21	α = 90
b = 32.56	β = 90.309
c = 72.61	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		2021-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.00	ELETTRA	11.2C

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	1.32	41.143	99.5	0.138	0.1	0.996	10.8	5.5		54908

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	1.32	1.35	100		0.862	0.57	0.704	2.2	5.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1JVT	1.32	41.14	54908	2648	99.471	0.21	0.2088	0.22	0.243	0.25	15.86

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]
-0.032		0.036	0.062		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.654
r_dihedral_angle_3_deg	14.29
r_dihedral_angle_4_deg	11.66
r_dihedral_angle_1_deg	7.654
r_lrange_it	4.998
r_lrange_other	4.748
r_angle_refined_deg	3.098
r_scangle_it	2.855
r_scangle_other	2.85
r_mcangle_it	2.36
r_mcangle_other	2.359
r_scbond_it	1.905
r_scbond_other	1.884
r_angle_other_deg	1.545
r_mcbond_it	1.525
r_mcbond_other	1.525
r_nbd_refined	0.198
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.183
r_symmetry_nbd_refined	0.173
r_xyhbond_nbd_refined	0.169
r_nbd_other	0.167
r_nbtor_refined	0.165
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.082
r_symmetry_xyhbond_nbd_other	0.08
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1902
Nucleic Acid Atoms
Solvent Atoms	387
Heterogen Atoms	26

Software

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