1H76

The crystal structure of diferric porcine serum transferrin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.3948

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 223.77α = 90
b = 44.89β = 105.39
c = 78.86γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATEMAR scanner 300 mm plateMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.5SRSPX9.5

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
12.1523.3960.07315.73.641503
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)
12.152.297.40.1238.13.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT0TFD2.1530380112001960.1360.182RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.593
r_scbond_it3.39
r_mcangle_it2.424
r_angle_other_deg1.961
r_dihedral_angle_3_deg1.364
r_mcbond_it1.313
r_symmetry_vdw_other0.389
r_symmetry_hbond_refined0.245
r_symmetry_vdw_refined0.24
r_nbd_refined0.224
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.593
r_scbond_it3.39
r_mcangle_it2.424
r_angle_other_deg1.961
r_dihedral_angle_3_deg1.364
r_mcbond_it1.313
r_symmetry_vdw_other0.389
r_symmetry_hbond_refined0.245
r_symmetry_vdw_refined0.24
r_nbd_refined0.224
r_nbd_other0.212
r_nbtor_other0.192
r_xyhbond_nbd_refined0.187
r_chiral_restr0.125
r_bond_refined_d0.023
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5233
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
XDISPdata reduction
SCALEPACKdata scaling
AMoREphasing