9THR | pdb_00009thr

Crystal structure of the human serum transferrin with Fe(III) bound at the C-lobe only (treated with DMSO)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4X1B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		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	67.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.098	α = 90
b = 156.774	β = 90
c = 107.108	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		2025-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97946	SOLEIL	PROXIMA 1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.2	74.32	93.7	0.995	12.4	10.6		18284

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	3.2	3.25			0.921

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	3.2	74.32	18209	914	93.75	0.183	0.1797	0.1827	0.2491	0.2489	44.185

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]
0.03			-0.04		0.009

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.28
r_dihedral_angle_4_deg	19.585
r_dihedral_angle_3_deg	19.579
r_dihedral_angle_1_deg	8.132
r_lrange_it	7.994
r_lrange_other	7.994
r_scangle_other	5.325
r_scangle_it	5.323
r_mcangle_it	5.199
r_mcangle_other	5.199
r_scbond_it	3.199
r_scbond_other	3.198
r_mcbond_it	3.172
r_mcbond_other	3.172
r_angle_refined_deg	1.567
r_angle_other_deg	1.247
r_nbd_refined	0.215
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.17
r_symmetry_nbd_refined	0.153
r_xyhbond_nbd_refined	0.144
r_nbd_other	0.142
r_metal_ion_refined	0.138
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.067
r_symmetry_xyhbond_nbd_other	0.055
r_symmetry_xyhbond_nbd_refined	0.041
r_bond_refined_d	0.007
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	5138
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	34

Software

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