28MS | pdb_000028ms

X-ray structure of the adduct between human serum transferrin with Fe3+ bound at the C-lobe and dirhodium tetraacetate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9THR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	15% (w/v) PEG 3350 16% (v/v) glycerol 8 mM disodium malonate 150 mM Na-PIPES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.776	α = 90
b = 157.085	β = 90
c = 107.559	γ = 90

Symmetry
Space Group	C 2 2 21

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 EIGER X 9M		2025-04-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.98011	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.368	103.58	92.8	0.205	0.996	10.3	13.4		33787

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.368	2.604	58.1		2.088	0.581	1.5	11.4

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	2.37	103.58	33785	1724	70.905	0.186	0.1829	0.1882	0.2443	0.2493	44.057

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]
-0.436			-0.013		0.449

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.741
r_dihedral_angle_2_deg	13.5
r_dihedral_angle_6_deg	13.325
r_lrange_other	10.241
r_lrange_it	10.229
r_scangle_it	8.267
r_scangle_other	8.165
r_dihedral_angle_1_deg	7.481
r_mcangle_it	6.481
r_mcangle_other	6.48
r_scbond_it	5.035
r_scbond_other	4.898
r_mcbond_it	4.102
r_mcbond_other	4.096
r_angle_refined_deg	1.781
r_angle_other_deg	0.583
r_nbd_refined	0.218
r_symmetry_xyhbond_nbd_refined	0.216
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.178
r_symmetry_nbd_refined	0.134
r_nbd_other	0.12
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.08
r_symmetry_xyhbond_nbd_other	0.08
r_metal_ion_refined	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_ext_dist_refined_b

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5201
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	71

Software

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