4X1D | pdb_00004x1d

Ytterbium-bound human serum transferrin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QYT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	0.1M PIPES, 17% PEG3350, 18% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.95	68.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.502	α = 90
b = 136.863	β = 90.41
c = 107.843	γ = 90

Symmetry
Space Group	C 1 2 1

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 315r		2013-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9793	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.8	50	99.7	0.09	0.103	0.05	8.7	4.2		56472

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	99.9		0.763	0.876	0.427	0.775		4.1	5644

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3QYT	2.8	50	50792	2627	95.43	0.1998	0.1983	0.1913	0.2307	0.2247	RANDOM	53.457

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]
0.36		-0.06	0.21		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.493
r_dihedral_angle_4_deg	18.736
r_dihedral_angle_3_deg	17.209
r_dihedral_angle_1_deg	6.615
r_mcangle_it	5.034
r_mcbond_it	3.107
r_mcbond_other	3.101
r_angle_refined_deg	1.391
r_angle_other_deg	0.867
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10214
Nucleic Acid Atoms
Solvent Atoms	139
Heterogen Atoms	28

Software

Software
Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing