2DWI | pdb_00002dwi

Crystal structure of the complex formed between C-terminal half of bovine lactoferrin and cellobiose at 2.2 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	298	0.1M MES, 25% POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, 0.01M ZINC SULPHATE, pH 6.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.472	α = 90
b = 50.439	β = 107.78
c = 65.93	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	298	IMAGE PLATE	MARRESEARCH	Mirror	2006-08-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5414

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	2.2	20	99.5	0.137	6.8		20292	20254			29.122

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	2.2	2.24	97.8		0.417	2.1

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	1NKX	2.2	20	20254	19604	650	99.45	0.18623	0.18566	0.18412	0.22068	RANDOM	30.249

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]
0.69		-1.32	-0.26		-1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.868
r_dihedral_angle_4_deg	21.702
r_dihedral_angle_3_deg	17.407
r_dihedral_angle_1_deg	6.149
r_scangle_it	5.241
r_scbond_it	3.261
r_mcangle_it	2.238
r_angle_refined_deg	1.441
r_mcbond_it	1.372
r_symmetry_vdw_refined	0.337
r_nbtor_refined	0.321
r_metal_ion_refined	0.245
r_symmetry_hbond_refined	0.241
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.182
r_chiral_restr	0.095
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2605
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	196

Software

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