9C9H | pdb_00009c9h

Interaction of chlorido(8-aminoquinoline)(pentamethylcyclopentadiene)rhodium(III) with HEWL

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4NHI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.7	294	Hen egg white lysozyme (100mg/mL), 0.8 M sodium chloride, and 0.1 M sodium acetate pH 4.7. Rh(III)(pentamethylcyclopentadiene)(8-aminoquinoline)chlorido (0.98 mg, 1 mg/mL) soak occurred in 0.8 M sodium nitrate and 0.1 M sodium acetate pH 4.7

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.007	α = 90
b = 79.007	β = 90
c = 37.952	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 210r		2020-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

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	1.25	39.535	100	0.138	0.14	0.019	0.999	18.1	52.8		33868

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.25	1.27			0.905	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.25	39.535	33808	1693	99.965	0.162	0.1602	0.1822	0.188	0.2071	16.868

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]
0.912			0.912		-1.825

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.843
r_dihedral_angle_6_deg	15.105
r_dihedral_angle_3_deg	13.36
r_lrange_it	11.428
r_lrange_other	11.257
r_scangle_it	7.273
r_scangle_other	7.269
r_dihedral_angle_1_deg	6.504
r_mcangle_other	6.239
r_mcangle_it	6.232
r_scbond_it	4.888
r_scbond_other	4.884
r_mcbond_it	4.253
r_mcbond_other	4.203
r_rigid_bond_restr	2.892
r_angle_refined_deg	2.439
r_angle_other_deg	0.724
r_symmetry_nbd_refined	0.355
r_nbd_other	0.291
r_nbd_refined	0.238
r_symmetry_nbd_other	0.2
r_symmetry_xyhbond_nbd_refined	0.184
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.138
r_symmetry_nbtor_other	0.11
r_chiral_restr	0.1
r_metal_ion_refined	0.044
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
Coot	model building