2O84

Crystal structure of K206E mutant of N-lobe human transferrin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A8EN-lobe human transferrin, PDB code 1A8E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4293Protein: 35mg/ml, 0.1M ammonium bicrbonate. Well: 18% PEG3350, 0.2M potassium acetate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.173α = 90
b = 57.317β = 90
c = 135.583γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMAR scanner 345 mm plateosmic mirrors2005-06-07MSINGLE 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
12.622.798.50.13993.3109171091732.58
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)
2.62.741000.37733.21576

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 REPLACEMENTTHROUGHOUTN-lobe human transferrin, PDB code 1A8E2.621.02103581035852197.990.2160.2160.2130.269RANDOM15.196
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]
0.020.07-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.633
r_dihedral_angle_4_deg20.708
r_dihedral_angle_3_deg16.26
r_dihedral_angle_1_deg5.392
r_scangle_it2.116
r_angle_refined_deg1.273
r_scbond_it1.257
r_mcangle_it0.868
r_mcbond_it0.46
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.633
r_dihedral_angle_4_deg20.708
r_dihedral_angle_3_deg16.26
r_dihedral_angle_1_deg5.392
r_scangle_it2.116
r_angle_refined_deg1.273
r_scbond_it1.257
r_mcangle_it0.868
r_mcbond_it0.46
r_nbtor_refined0.306
r_symmetry_hbond_refined0.219
r_nbd_refined0.205
r_symmetry_vdw_refined0.205
r_xyhbond_nbd_refined0.147
r_chiral_restr0.087
r_metal_ion_refined0.045
r_bond_refined_d0.01
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2551
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms6

Software

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