2E1S

Crystal structure of the complex of C-terminal half of bovine lactoferrin and arabinose at 2.7 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NKX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52980.1M MES, 25% POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, 0.01M ZINC SULPHATE, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6553.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.349α = 90
b = 50.308β = 107.79
c = 65.851γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMirror2006-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5414

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
12.72099.10.146.51095210952
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)
12.72.75970.3071.9

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 REPLACEMENTTHROUGHOUT1NKX2.720109521027651697.810.209120.207810.205570.23301RANDOM19.162
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]
0.67-1.04-0.53-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.577
r_dihedral_angle_4_deg20.024
r_dihedral_angle_3_deg18.036
r_dihedral_angle_1_deg5.788
r_scangle_it5.339
r_scbond_it3.373
r_mcangle_it2.476
r_angle_refined_deg1.82
r_mcbond_it1.469
r_nbtor_refined0.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.577
r_dihedral_angle_4_deg20.024
r_dihedral_angle_3_deg18.036
r_dihedral_angle_1_deg5.788
r_scangle_it5.339
r_scbond_it3.373
r_mcangle_it2.476
r_angle_refined_deg1.82
r_mcbond_it1.469
r_nbtor_refined0.324
r_symmetry_vdw_refined0.27
r_nbd_refined0.254
r_symmetry_hbond_refined0.25
r_xyhbond_nbd_refined0.175
r_metal_ion_refined0.152
r_chiral_restr0.104
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2605
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms183

Software

Software
Software NamePurpose
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling
AMoREphasing