2O7U

Crystal structure of K206E/K296E mutant of the N-terminal half molecule of human transferrin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A8EWild type transferrin. PDB entry code 1A8E.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4291Protein: 35mg/ml, 0.1M ammonium bicarbonate. Well: 20% PEG 3350, 0.2 M potassium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6353.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.462α = 90
b = 97.897β = 90.01
c = 208.953γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 345 mm plateOsmic mirrors2006-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.84898.50.07416.43.38330683306
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9598.80.4063.23.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTWild type transferrin. PDB entry code 1A8E.2.829.768214478012413297.330.231090.229610.25885RANDOM57.888
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]
0.140.2-0.280.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.16
r_dihedral_angle_4_deg18.612
r_dihedral_angle_3_deg17.55
r_dihedral_angle_1_deg5.993
r_scangle_it2.313
r_angle_refined_deg1.323
r_scbond_it1.299
r_mcangle_it0.854
r_mcbond_it0.44
r_symmetry_vdw_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.16
r_dihedral_angle_4_deg18.612
r_dihedral_angle_3_deg17.55
r_dihedral_angle_1_deg5.993
r_scangle_it2.313
r_angle_refined_deg1.323
r_scbond_it1.299
r_mcangle_it0.854
r_mcbond_it0.44
r_symmetry_vdw_refined0.317
r_nbtor_refined0.31
r_symmetry_hbond_refined0.286
r_nbd_refined0.222
r_xyhbond_nbd_refined0.148
r_chiral_restr0.093
r_metal_ion_refined0.084
r_bond_refined_d0.011
r_gen_planes_refined0.004
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 Atoms22950
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms45

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
CCP4data scaling