2FA7 | pdb_00002fa7

Crystal structure of the complex of bovine lactoferrin C-lobe with a pentasaccharide at 2.38 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B6D	PDB ENTRY 2B6D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1M MES, PEG MONOMETHYLETHER, 0.1M ZNSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.96	α = 90
b = 50.499	β = 107.5
c = 65.859	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	MARRESEARCH	Mirror	2005-10-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.38	63.24	86.8			16044	16044

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.38	2.42	96.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2B6D	2.38	62.02	16044	14993	484	96.47	0.213	0.19948	0.19831	0.23581	RANDOM	33.509

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]
0.89		-1.11	-0.56		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.743
r_dihedral_angle_1_deg	5.419
r_scangle_it	3.675
r_scbond_it	2.074
r_angle_refined_deg	1.898
r_mcangle_it	1.451
r_mcbond_it	0.749
r_symmetry_hbond_refined	0.381
r_symmetry_vdw_refined	0.292
r_nbd_refined	0.283

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.743
r_dihedral_angle_1_deg	5.419
r_scangle_it	3.675
r_scbond_it	2.074
r_angle_refined_deg	1.898
r_mcangle_it	1.451
r_mcbond_it	0.749
r_symmetry_hbond_refined	0.381
r_symmetry_vdw_refined	0.292
r_nbd_refined	0.283
r_xyhbond_nbd_refined	0.205
r_metal_ion_refined	0.175
r_chiral_restr	0.142
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2604
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	244

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.