7EQU

Crystal structure of the C-lobe of lactoferrin produced by limited proteolysis using pepsin at 2.74A resolution

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5HBC

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
3.52	65.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.759	α = 90
b = 81.554	β = 129.949
c = 111.364	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		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)	Rrim I (All)	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	2.74	76.85	97.5	0.06	0.07	0.99	10.2	2.9		27187

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.74	2.79			0.03	0.04	0.99

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	NONE	5HBC	2.743	76.846	27050	1361	96.995	0.242	0.2388	0.2984	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]
2.535		2.636	-13.1		2.559

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.207
r_dihedral_angle_4_deg	22.618
r_dihedral_angle_3_deg	21.628
r_lrange_it	15.116
r_lrange_other	15.114
r_mcangle_it	11.547
r_mcangle_other	11.545
r_scangle_it	11.027
r_scangle_other	11.026
r_mcbond_it	7.75
r_mcbond_other	7.749
r_scbond_it	7.218
r_scbond_other	7.218
r_dihedral_angle_1_deg	6.843
r_angle_refined_deg	1.681
r_angle_other_deg	1.199
r_nbd_other	0.299
r_symmetry_nbd_refined	0.253
r_nbd_refined	0.214
r_symmetry_nbd_other	0.21
r_symmetry_xyhbond_nbd_refined	0.202
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.163
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.062
r_chiral_restr	0.056
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5316
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	221

Software

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