9THQ | pdb_00009thq

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

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
3.91	68.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.232	α = 90
b = 158.132	β = 90
c = 107.708	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 EIGER2 S 16M		2025-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.99987	MAX IV	BioMAX

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	2.44	79.1	96.4	0.987	7.8	8.2		42667

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	2.44	2.51			0.471

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	2.44	79.1	42666	2117	96.503	0.19	0.1878	0.193	0.2309	0.2291	35.412

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]
-0.277			0.153		0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.117
r_dihedral_angle_4_deg	22.036
r_dihedral_angle_3_deg	17.813
r_lrange_it	9.245
r_lrange_other	9.241
r_dihedral_angle_1_deg	7.343
r_scangle_it	6.624
r_scangle_other	6.61
r_mcangle_it	5.546
r_mcangle_other	5.546
r_scbond_it	4.216
r_scbond_other	4.148
r_mcbond_it	3.517
r_mcbond_other	3.517
r_angle_refined_deg	1.714
r_angle_other_deg	1.339
r_nbd_refined	0.204
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.153
r_metal_ion_refined	0.132
r_symmetry_xyhbond_nbd_refined	0.129
r_nbd_other	0.115
r_symmetry_nbd_refined	0.102
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.081
r_symmetry_xyhbond_nbd_other	0.02
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5201
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	64

Software

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