4G4C

Room temperature X-ray diffraction study of carboplatin binding to HEWL in DMSO media after 13 months of crystal storage


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2W1YPDB ENTRY 2W1Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH4.7295HEWL co-crystallized with carboplatin (with DMSO added) in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7, BATCH, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0740.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.231α = 90
b = 79.231β = 90
c = 37.89γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295CCDAPEX II CCD2012-01-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
1256.025520.1571818.315602817042
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)
122.0397.50.8554.110

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2W1Y256.0252415602817040499.830.162490.160610.20319RANDOM19.186
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]
-0.17-0.170.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.262
r_dihedral_angle_4_deg21.899
r_dihedral_angle_3_deg16.098
r_dihedral_angle_1_deg6.76
r_angle_refined_deg1.831
r_angle_other_deg1.096
r_chiral_restr0.122
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.262
r_dihedral_angle_4_deg21.899
r_dihedral_angle_3_deg16.098
r_dihedral_angle_1_deg6.76
r_angle_refined_deg1.831
r_angle_other_deg1.096
r_chiral_restr0.122
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.001
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms17

Software

Software
Software NamePurpose
APEXdata collection
PHASERphasing
REFMACrefinement
EVAL15data reduction
EVAL15data scaling