9H4V

Crystal structure of the adduct formed upon reaction of aurothiomalate with human serum transferrin (apo-form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7Q1L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29320% w/v PEG 3350 and 200 mM trisodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.7755.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.472α = 90
b = 99.714β = 90
c = 198.388γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2023-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8731ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
13.0289.2510017.813.133617
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.023.071000.41.313.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.0289.2531963159599.770.245780.243250.24720.29650.3RANDOM84.632
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]
-5.18-0.255.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg13.399
r_long_range_B_refined7.538
r_dihedral_angle_1_deg6.056
r_mcangle_it3.032
r_dihedral_angle_2_deg2.976
r_mcbond_it1.644
r_scbond_it1.454
r_angle_refined_deg0.96
r_chiral_restr0.084
r_bond_refined_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10488
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms137

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing