2DOJ

Crystal structure of the complex of C-terminal lobe of bovine lactoferrin with adenosine at 2.4 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	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
2.66	53.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.317	α = 90
b = 50.465	β = 107.66
c = 65.919	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	291	IMAGE PLATE	MAR scanner 345 mm plate		2006-02-22	M	SINGLE WAVELENGTH

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

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	2.4	63.25	97.6			15352	15352

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	2.4	2.43	99.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2B6D	2.4	20	15352	14577	767	97.42	0.2	0.19387	0.19238	0.22267	RANDOM	29.55

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]
-0.29		-1.26	-0.18		-0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.277
r_dihedral_angle_1_deg	5.284
r_scangle_it	3.748
r_scbond_it	2.168
r_angle_refined_deg	1.945
r_mcangle_it	1.561
r_mcbond_it	0.825
r_nbd_refined	0.248
r_symmetry_vdw_refined	0.234
r_symmetry_hbond_refined	0.195

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.277
r_dihedral_angle_1_deg	5.284
r_scangle_it	3.748
r_scbond_it	2.168
r_angle_refined_deg	1.945
r_mcangle_it	1.561
r_mcbond_it	0.825
r_nbd_refined	0.248
r_symmetry_vdw_refined	0.234
r_symmetry_hbond_refined	0.195
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.125
r_metal_ion_refined	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2605
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	170

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.