2Q8J

Crystal Structure of the complex of C-lobe of bovine lactoferrin with Mannitol and Mannose at 2.7 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DWH	pdb entry 2DWH

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
2.63	53.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.4	α = 90
b = 50.3	β = 107.8
c = 65.9	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	2007-04-26	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)	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	2.7	20	94.4	0.147	4.8	6.36		9718

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	2.7	2.8	95.2		0.438	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 2DWH	2.71	20	9718	467	94.4	0.19719	0.19491	0.23983	RANDOM	26.682

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]
1.48		0.25	-0.38		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.026
r_dihedral_angle_3_deg	20.337
r_dihedral_angle_4_deg	19.984
r_dihedral_angle_1_deg	6.069
r_scangle_it	4.805
r_scbond_it	2.939
r_mcangle_it	2.279
r_angle_refined_deg	2.276
r_mcbond_it	1.577
r_symmetry_vdw_refined	0.375

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.026
r_dihedral_angle_3_deg	20.337
r_dihedral_angle_4_deg	19.984
r_dihedral_angle_1_deg	6.069
r_scangle_it	4.805
r_scbond_it	2.939
r_mcangle_it	2.279
r_angle_refined_deg	2.276
r_mcbond_it	1.577
r_symmetry_vdw_refined	0.375
r_nbtor_refined	0.326
r_nbd_refined	0.271
r_metal_ion_refined	0.24
r_xyhbond_nbd_refined	0.216
r_symmetry_hbond_refined	0.203
r_chiral_restr	0.13
r_bond_refined_d	0.024
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2604
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	117

Software

Software
Software Name	Purpose
REFMAC	refinement
AUTOMAR	data collection
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.