3TAJ

Crystal structure of C-lobe of bovine lactoferrin complexed with Nabumetone at 1.7A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O97

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
2.53	51.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.347	α = 90
b = 49.826	β = 106.63
c = 65.068	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	1.7	62.35	99.8	0.047	27		41412	41412			20.2

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	1.7	1.73	97.2		0.325	2.3

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	3O97	1.7	50	41412	39257	2082	99.58	0.2031	0.20293	0.20182	0.22329	RANDOM	26.934

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]
0.9		-1.15	-1.01		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.863
r_dihedral_angle_4_deg	16.621
r_dihedral_angle_3_deg	14.161
r_dihedral_angle_1_deg	5.702
r_scangle_it	2.091
r_mcangle_it	1.243
r_scbond_it	1.171
r_angle_refined_deg	1.099
r_mcbond_it	0.663
r_chiral_restr	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.863
r_dihedral_angle_4_deg	16.621
r_dihedral_angle_3_deg	14.161
r_dihedral_angle_1_deg	5.702
r_scangle_it	2.091
r_mcangle_it	1.243
r_scbond_it	1.171
r_angle_refined_deg	1.099
r_mcbond_it	0.663
r_chiral_restr	0.07
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2604
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	99

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.