7ENU

Crystal structure of iron-saturated C-terminal half of lactoferrin produced proteolytically using pepsin at 2.32A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	Magnesium acetate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.67	α = 90
b = 82.027	β = 129.624
c = 112.137	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	PIXEL	DECTRIS PILATUS 6M-F	MIRROR	2021-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.9655	ESRF	ID30B

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	2.32	86.38	98.8	0.036	0.99	15.1	3		47113

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	2.32	2.38	99.7		0.47	0.91	2.3	2.9

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1BLF	2.322	77.748	46529	2275	98.75	0.205	0.2029	0.2487	70

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]
4.514		1.272	-7.93		0.552

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.083
r_dihedral_angle_4_deg	21.809
r_dihedral_angle_3_deg	18.796
r_lrange_it	12.414
r_lrange_other	12.413
r_scangle_it	10.156
r_scangle_other	10.155
r_mcangle_it	8.763
r_mcangle_other	8.762
r_dihedral_angle_1_deg	7.744
r_scbond_it	6.897
r_scbond_other	6.896
r_mcbond_it	6.212
r_mcbond_other	6.206
r_angle_refined_deg	1.706
r_angle_other_deg	1.257
r_symmetry_xyhbond_nbd_refined	0.243
r_nbd_other	0.223
r_nbd_refined	0.206
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.161
r_xyhbond_nbd_refined	0.158
r_symmetry_nbd_refined	0.145
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.066
r_symmetry_xyhbond_nbd_other	0.038
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5314
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	244

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing