9H49 | pdb_00009h49

Crystal structure of the adduct between human serum transferrin (apo-form) and cisplatin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729320% w/v PEG 3350 and 200 mM ammonium citrate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.0459.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.184α = 90
b = 103.68β = 90
c = 200.283γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X CdTe 16M2023-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.8856ESRFID23-1

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
13.5280.8410017.610.923356
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)
13.523.581000.40.811.3

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 REPLACEMENTTHROUGHOUT3.5280.8421987117799.170.231520.230570.23110.249360.2498RANDOM161.713
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]
0.146.76-6.9
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined13.169
r_dihedral_angle_3_deg12.879
r_mcangle_it6.915
r_dihedral_angle_1_deg6.105
r_scbond_it4.08
r_mcbond_it3.948
r_dihedral_angle_2_deg2.703
r_angle_refined_deg0.936
r_chiral_restr0.081
r_bond_refined_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined13.169
r_dihedral_angle_3_deg12.879
r_mcangle_it6.915
r_dihedral_angle_1_deg6.105
r_scbond_it4.08
r_mcbond_it3.948
r_dihedral_angle_2_deg2.703
r_angle_refined_deg0.936
r_chiral_restr0.081
r_bond_refined_d0.002
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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_it
r_scangle_other
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 Atoms10496
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing