3VDF

Crystal Structure of C-lobe of Bovine lactoferrin Complexed with diaminopimelic acid at 1.46 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IB0PDB ENTRY 3IB0

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
2.652.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.212α = 90
b = 50.023β = 107
c = 65.206γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHmirror2011-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

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
11.4662.299.40.04727.96608466074
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)
11.461.4997.90.4792

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3IB01.4637.876608462718335699.20.162070.162070.160370.19395RANDOM22.269
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]
0.56-0.49-0.5-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.505
r_dihedral_angle_4_deg18.491
r_dihedral_angle_3_deg13.27
r_dihedral_angle_1_deg6.685
r_angle_refined_deg2.693
r_chiral_restr0.164
r_bond_refined_d0.028
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms455
Heterogen Atoms95

Software

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