7FDW

Crystal structure of pepsin cleaved lactoferrin C-lobe at 2.28 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BLF

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
3.55	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.781	α = 90
b = 81.703	β = 129.857
c = 111.694	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 BM30A	0.96546	ESRF	BM30A

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	2.277	76.7	98.8	0.03	0.97	17.6	3		48821

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	2.277	2.31	99.8		0.44	0.94	2.9	3.2

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	2.277	76.7	48241	2465	98.814	0.214	0.2126	0.2469	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]
0.788		0.92	-8.288		2.492

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.295
r_dihedral_angle_4_deg	20.238
r_dihedral_angle_3_deg	18.013
r_lrange_other	15.265
r_lrange_it	15.244
r_scangle_other	10.378
r_scangle_it	10.376
r_mcangle_it	9.995
r_mcangle_other	9.993
r_dihedral_angle_1_deg	7.46
r_mcbond_it	7.176
r_mcbond_other	7.169
r_scbond_other	7.116
r_scbond_it	7.114
r_angle_other_deg	2.518
r_angle_refined_deg	1.607
r_nbd_other	0.271
r_symmetry_xyhbond_nbd_other	0.231
r_symmetry_nbd_other	0.23
r_nbd_refined	0.202
r_symmetry_nbd_refined	0.198
r_xyhbond_nbd_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.163
r_ncsr_local_group_1	0.082
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.066
r_bond_other_d	0.036
r_metal_ion_refined	0.012
r_bond_refined_d	0.009
r_gen_planes_other	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5314
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	155

Software

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