7R1P | pdb_00007r1p

X-ray structure of the adduct formed upon reaction of the gold(I) N-heterocyclic carbene complex Au1 with RNase A

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 pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.72	α = 90
b = 32.72	β = 90.261
c = 72.71	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		2021-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.96	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.42	50.36	96.1	0.073	0.08	0.031	0.998	12.9	6.4		43467

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.45	94.2		0.599	0.661	0.248	0.807	3.6	6.7

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	1.42	50.36	43467		96.068	0.191	0.1893	0.2	0.219	0.23	23.39

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]
0.019		0.084	-0.063		0.043

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.161
r_dihedral_angle_3_deg	13.492
r_dihedral_angle_4_deg	12.836
r_dihedral_angle_1_deg	7.061
r_lrange_it	6.924
r_lrange_other	6.852
r_scangle_it	4.526
r_scangle_other	4.504
r_mcangle_it	3.594
r_mcangle_other	3.593
r_scbond_it	2.987
r_scbond_other	2.964
r_mcbond_it	2.338
r_mcbond_other	2.338
r_angle_refined_deg	1.791
r_angle_other_deg	1.544
r_symmetry_nbd_refined	0.221
r_nbd_other	0.219
r_nbd_refined	0.21
r_symmetry_nbd_other	0.186
r_symmetry_xyhbond_nbd_refined	0.186
r_xyhbond_nbd_refined	0.172
r_nbtor_refined	0.165
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1902
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	7

Software

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