3TOD

Crystal Structure of C-lobe of Bovine lactoferrin Complexed with 1-Butyl-1H-Pyrazole-5-carboxylic acid at 1.38 A Resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IB0

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
2.61	52.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.415	α = 90
b = 49.977	β = 107.14
c = 65.289	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	77	CCD	MARRESEARCH	Mirror	2011-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	1.38	62.39	97.2	0.0802	18.2		79168	72933			23.2

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	1.38	1.43	91.5		0.389	3

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	3IB0	1.38	62.39	79168	72933	3867	97.01	0.20156	0.20156	0.19969	0.23621	RANDOM	23.178

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]
-0.03		-0.65	-0.74		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.746
r_dihedral_angle_4_deg	17.933
r_dihedral_angle_3_deg	13.161
r_dihedral_angle_1_deg	6.599
r_scangle_it	5.672
r_scbond_it	3.644
r_mcangle_it	2.69
r_angle_refined_deg	2.422
r_mcbond_it	1.695
r_chiral_restr	0.159

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.746
r_dihedral_angle_4_deg	17.933
r_dihedral_angle_3_deg	13.161
r_dihedral_angle_1_deg	6.599
r_scangle_it	5.672
r_scbond_it	3.644
r_mcangle_it	2.69
r_angle_refined_deg	2.422
r_mcbond_it	1.695
r_chiral_restr	0.159
r_bond_refined_d	0.03
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2605
Nucleic Acid Atoms
Solvent Atoms	549
Heterogen Atoms	126

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	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.