4NSI

Carboplatin binding to HEWL in 20% propanol, 20% PEG 4000 at pH5.6


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.629820mg of HEWL (0.6mM) was dissolved in 1ml distilled water. 1.4mg of carboplatin (1.8mM) was added along with 75 l DMSO. 2 l of this was mixed with 2 l of resevoir solution 20% PEG 4000 at pH5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9436.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.713α = 90
b = 77.713β = 90
c = 36.84γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPEX II CCD2013-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H1.5418

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
12.333.3153.60.2957.57.89485508642
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)
12.32.651000.5051.57.2

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2W1Y2.333.31249485508627099.930.2240.223520.220250.28489RANDOM29.538
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]
-0.48-0.480.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.089
r_dihedral_angle_4_deg15.927
r_dihedral_angle_3_deg14.072
r_dihedral_angle_1_deg6.73
r_long_range_B_refined5.116
r_long_range_B_other5.113
r_scangle_other3.168
r_mcangle_other2.715
r_mcangle_it2.711
r_mcbond_it1.653
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.089
r_dihedral_angle_4_deg15.927
r_dihedral_angle_3_deg14.072
r_dihedral_angle_1_deg6.73
r_long_range_B_refined5.116
r_long_range_B_other5.113
r_scangle_other3.168
r_mcangle_other2.715
r_mcangle_it2.711
r_mcbond_it1.653
r_scbond_it1.65
r_scbond_other1.639
r_mcbond_other1.637
r_angle_refined_deg1.373
r_angle_other_deg0.846
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
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_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 Atoms37
Heterogen Atoms31

Software

Software
Software NamePurpose
APEXdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
APEXdata reduction