9XXU | pdb_00009xxu

Crystal structure of the chymotrypsin-cleaved iron-free C-lobe of bovine lactoferrin at 2.82 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		the structure was solved using the molecular replacement method using the auto-MR tool employing MrBUMP with MorDa within the CCP4 cloud server. the initial search model obtained was subjected to several refinement cycles to obtain the final solution.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	0.1M Sodium acetate trihydrate (pH 4.6), 0.2M ammonium sulfate, 25% w/v PEG 2000

Crystal Properties
Matthews coefficient	Solvent content
2.6	53.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.684	α = 90
b = 139.06	β = 90
c = 120.741	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 X 9M		2023-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.8731	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	2.82	47.583	99.6	0.155	0.096	0.995	8.3	6.7		19057			72.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.82	2.97	99.8		1.497	0.912	0.535	1.2	7

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	2.82	47.583	19046	371	99.343	0.213	0.2114	0.2156	0.2686	0.27	79.726

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]
3.317			-3.681		0.363

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	15.334
r_lrange_it	15.333
r_dihedral_angle_3_deg	14.79
r_dihedral_angle_6_deg	13.386
r_dihedral_angle_2_deg	10.706
r_scangle_it	9.47
r_scangle_other	9.461
r_mcangle_it	8.078
r_mcangle_other	8.077
r_dihedral_angle_1_deg	7.617
r_scbond_it	5.777
r_scbond_other	5.766
r_mcbond_it	5.065
r_mcbond_other	5.065
r_angle_other_deg	1.897
r_angle_refined_deg	1.506
r_nbd_refined	0.236
r_symmetry_nbd_other	0.222
r_nbd_other	0.186
r_symmetry_nbd_refined	0.181
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.135
r_symmetry_nbtor_other	0.102
r_symmetry_xyhbond_nbd_other	0.031
r_gen_planes_other	0.024
r_gen_planes_refined	0.012
r_bond_refined_d	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5182
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	333

Software

Software
Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data reduction
autoPROC	data scaling
MOLREP	phasing
Coot	model building