28MR | pdb_000028mr

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

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
3.82	67.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.936	α = 90
b = 156.712	β = 90
c = 107.145	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 16M		2023-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 1

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	2.262	103.116	93.9	0.208	0.997	9.8	12.6		30700

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	2.262	2.502			0.734

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	2.262	103.116	30700	1528	56.823	0.182	0.1791	0.1853	0.2344	0.2375	44.34

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]
-0.458			-0.335		0.793

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.681
r_dihedral_angle_6_deg	13.802
r_lrange_it	10.186
r_lrange_other	10.166
r_dihedral_angle_2_deg	9.091
r_dihedral_angle_1_deg	7.569
r_scangle_it	7.207
r_scangle_other	7.206
r_mcangle_it	6.109
r_mcangle_other	6.108
r_scbond_it	4.286
r_scbond_other	4.285
r_mcbond_it	3.764
r_mcbond_other	3.761
r_angle_refined_deg	1.487
r_angle_other_deg	0.528
r_nbd_refined	0.222
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.175
r_nbd_other	0.132
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_nbd_refined	0.106
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.069
r_metal_ion_refined	0.059
r_symmetry_xyhbond_nbd_other	0.036
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5201
Nucleic Acid Atoms
Solvent Atoms	383
Heterogen Atoms	20

Software

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