2Q8J

Crystal Structure of the complex of C-lobe of bovine lactoferrin with Mannitol and Mannose at 2.7 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DWHpdb entry 2DWH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M MES, PEG MONOMETHYLETHER, 0.1M ZNSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6353.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.4α = 90
b = 50.3β = 107.8
c = 65.9γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMirror2007-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

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
12.72094.40.1474.86.369718
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)
12.72.895.20.4381.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2DWH2.7120971846794.40.197190.194910.23983RANDOM26.682
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]
1.480.25-0.38-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.026
r_dihedral_angle_3_deg20.337
r_dihedral_angle_4_deg19.984
r_dihedral_angle_1_deg6.069
r_scangle_it4.805
r_scbond_it2.939
r_mcangle_it2.279
r_angle_refined_deg2.276
r_mcbond_it1.577
r_symmetry_vdw_refined0.375
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.026
r_dihedral_angle_3_deg20.337
r_dihedral_angle_4_deg19.984
r_dihedral_angle_1_deg6.069
r_scangle_it4.805
r_scbond_it2.939
r_mcangle_it2.279
r_angle_refined_deg2.276
r_mcbond_it1.577
r_symmetry_vdw_refined0.375
r_nbtor_refined0.326
r_nbd_refined0.271
r_metal_ion_refined0.24
r_xyhbond_nbd_refined0.216
r_symmetry_hbond_refined0.203
r_chiral_restr0.13
r_bond_refined_d0.024
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
AUTOMARdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing