7QPZ | pdb_00007qpz

X-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] with RNase A (4)

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	44.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.73	α = 90
b = 32.87	β = 90.154
c = 72.89	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	1.45	50.86	99.9	0.185	0.135	0.988	11.8	5.2		43428

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	1.45	1.48	100		0.796	0.557	0.67	3.1	5.6

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	1.45	50.855	42535	2090	99.256	0.164	0.1619	0.17	0.2019	0.21	16.092

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]
-0.026		0.052	0.053		-0.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.731
r_dihedral_angle_3_deg	13.323
r_dihedral_angle_4_deg	12.896
r_dihedral_angle_1_deg	7.769
r_lrange_it	7.44
r_lrange_other	7.201
r_scangle_other	3.481
r_scangle_it	3.458
r_mcangle_it	2.878
r_mcangle_other	2.877
r_angle_refined_deg	2.801
r_scbond_it	2.282
r_scbond_other	2.265
r_mcbond_it	1.768
r_mcbond_other	1.768
r_angle_other_deg	1.549
r_nbd_refined	0.238
r_symmetry_xyhbond_nbd_other	0.225
r_symmetry_nbd_other	0.188
r_xyhbond_nbd_refined	0.183
r_nbd_other	0.18
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.147
r_symmetry_nbd_refined	0.132
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1882
Nucleic Acid Atoms
Solvent Atoms	436
Heterogen Atoms	47

Software

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