7QHR

Unexpected imidazole coordination to dirhodium tetraacetate complex in a protein environment: insights from X-ray crystallography and quantum chemistry

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.1	298	22% PEG 4000 10 mM sodium citrate pH 5.1

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.5	α = 90
b = 32.53	β = 90.295
c = 72.2	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		2021-03-03	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)	Rrim 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	1.4	50.3	94.3	0.058	1	15.4	6.4		43550

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.43	87.91		1.079	0.8	2.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1JVT	1.4	50.3	43550	2039	94.3	0.192	0.1897	0.231	24.977

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]
-0.139		0.101	-0.14		0.278

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.674
r_dihedral_angle_4_deg	14.44
r_dihedral_angle_3_deg	13.801
r_lrange_it	7.546
r_lrange_other	7.54
r_dihedral_angle_1_deg	7.203
r_scangle_it	4.65
r_scangle_other	4.566
r_angle_refined_deg	3.948
r_mcangle_it	3.747
r_mcangle_other	3.746
r_scbond_it	3.147
r_scbond_other	3.105
r_mcbond_it	2.527
r_mcbond_other	2.527
r_angle_other_deg	1.517
r_symmetry_xyhbond_nbd_refined	0.237
r_nbd_other	0.204
r_nbd_refined	0.203
r_symmetry_nbd_other	0.183
r_xyhbond_nbd_refined	0.18
r_symmetry_nbd_refined	0.177
r_nbtor_refined	0.167
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_gen_planes_other	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1898
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	67

Software

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