4X1B

Human serum transferrin with ferric ion bound at the C-lobe only


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QYT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62980.1M PIPES, 17% PEG3350, 18% Glycerol
Crystal Properties
Matthews coefficientSolvent content
3.9969.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.056α = 90
b = 156.649β = 90
c = 107.162γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97852SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.455099.90.0750.0810.0310.47.442808
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.541000.7370.7920.2890.9057.54210

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 REPLACEMENTTHROUGHOUT3QYT2.455039358207497.060.19180.190.2265RANDOM55.587
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]
-0.80.150.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.962
r_dihedral_angle_4_deg18.297
r_dihedral_angle_3_deg15.02
r_dihedral_angle_1_deg6.119
r_mcangle_it1.967
r_mcbond_it1.189
r_angle_refined_deg1.188
r_mcbond_other1.188
r_angle_other_deg0.778
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.962
r_dihedral_angle_4_deg18.297
r_dihedral_angle_3_deg15.02
r_dihedral_angle_1_deg6.119
r_mcangle_it1.967
r_mcbond_it1.189
r_angle_refined_deg1.188
r_mcbond_other1.188
r_angle_other_deg0.778
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5045
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms14

Software

Software
Software NamePurpose
DENZOdata collection
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing