3K0V | pdb_00003k0v

Removal of sugars and sugars-like molecules from the solution by C-lobe of lactoferrin: Crystal structure of the complex of C-lobe with beta-D-glucopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-alpha-D-glucopyranose at 1.9 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IBO	pdb entry 3IBO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.01M Znso4, 0.1M MES, 25% PEG, Monomethyl Ether 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.81	α = 90
b = 50.134	β = 107.1
c = 65.545	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	300	IMAGE PLATE	MARRESEARCH	MIRROR	2009-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	1.91	62.62	96	0.058	7.1		29538	29538

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	1.96	99.1		0.104	2.5

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3IBO	1.91	62	28296	26864	1432	94.54	0.20884	0.20677	0.22	0.23685	0.25	RANDOM	25.247

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]
1.06		-0.62	-0.93		-0.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.332
r_dihedral_angle_4_deg	19.535
r_dihedral_angle_3_deg	16.642
r_dihedral_angle_1_deg	5.889
r_scangle_it	2.51
r_scbond_it	1.579
r_angle_refined_deg	1.28
r_mcangle_it	1.17
r_mcbond_it	0.681
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.332
r_dihedral_angle_4_deg	19.535
r_dihedral_angle_3_deg	16.642
r_dihedral_angle_1_deg	5.889
r_scangle_it	2.51
r_scbond_it	1.579
r_angle_refined_deg	1.28
r_mcangle_it	1.17
r_mcbond_it	0.681
r_nbtor_refined	0.303
r_symmetry_hbond_refined	0.292
r_symmetry_vdw_refined	0.279
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.086
r_metal_ion_refined	0.034
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2604
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	152

Software

Software
Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

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.