7QPW | pdb_00007qpw

X-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] with RNase A (1)

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	298	22 % PEG 4K 0.01 M sodium citrate pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.5	α = 90
b = 32.91	β = 90.164
c = 73.06	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	1.15	73.06	99.6	0.078	0.051	0.997	10.3	6.1		84723

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	1.15	1.17	100		0.699	0.479	0.738	2.2	5.4

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	1.15	73.06	84723	4156	99.6	0.137	0.136	0.14	0.1654	0.17	17.985

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]
-0.771		0.508	0.268		0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.841
r_dihedral_angle_3_deg	12.296
r_dihedral_angle_4_deg	11.199
r_rigid_bond_restr	7.571
r_dihedral_angle_1_deg	7.34
r_lrange_it	6.318
r_lrange_other	5.841
r_scangle_it	5.537
r_scangle_other	5.537
r_scbond_it	4.735
r_scbond_other	4.731
r_mcangle_it	4.315
r_mcangle_other	4.313
r_mcbond_other	4.3
r_mcbond_it	4.298
r_angle_refined_deg	3.404
r_angle_other_deg	1.659
r_nbd_refined	0.285
r_nbd_other	0.23
r_symmetry_nbd_other	0.214
r_symmetry_nbd_refined	0.206
r_xyhbond_nbd_refined	0.177
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.167
r_chiral_restr	0.11
r_symmetry_nbtor_other	0.09
r_bond_refined_d	0.018
r_symmetry_xyhbond_nbd_other	0.016
r_gen_planes_refined	0.014
r_gen_planes_other	0.005
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1881
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms	45

Software

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