3SDF

Crystal Structure of C-lobe of Bovine lactoferrin Complexed with Lipoteichoic acid at 2.1 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RGY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.01M Znso4, 0.1M MES, 25% PEG, Monomethyl Ether 550 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6753.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.417α = 90
b = 50.398β = 107.72
c = 65.944γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300IMAGE PLATEMARRESEARCHmirror2011-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.541

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.162.8294.30.05912214752124431.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1894.50.2722

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3RGY2.1622147521244116795.740.19910.19910.197080.23441RANDOM36.118
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]
0.07-1.26-0.67-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.785
r_dihedral_angle_4_deg15.135
r_dihedral_angle_3_deg14.396
r_dihedral_angle_1_deg4.025
r_scangle_it1.807
r_angle_refined_deg1.246
r_mcangle_it1.168
r_scbond_it1.033
r_mcbond_it0.628
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.785
r_dihedral_angle_4_deg15.135
r_dihedral_angle_3_deg14.396
r_dihedral_angle_1_deg4.025
r_scangle_it1.807
r_angle_refined_deg1.246
r_mcangle_it1.168
r_scbond_it1.033
r_mcbond_it0.628
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms147

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling