4NSG

Carboplatin binding to HEWL in NaBr crystallisation conditions studied at an X-ray wavelength of 1.5418A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Batch4.729420mg HEWL co-crystallised with 1.4mg carboplatin with 75 l DMSO, 462.5 l 0.1M NaAc and 462.5 l 1M NaBr solution., pH 4.7, Batch, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
1.9938.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.377α = 90
b = 78.377β = 90
c = 37.213γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPEX II CCD2013-10-02MSINGLE 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
1255.4294.60.22410.818.18110767542
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)
122.185.90.6191.33.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 2W1Y255.428110767537697.470.221210.218860.27085RANDOM13.759
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]
-0.19-0.190.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.262
r_dihedral_angle_4_deg18.457
r_dihedral_angle_3_deg12.721
r_dihedral_angle_1_deg5.272
r_long_range_B_refined2.421
r_long_range_B_other2.42
r_angle_refined_deg0.685
r_mcangle_it0.574
r_mcangle_other0.574
r_angle_other_deg0.536
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.262
r_dihedral_angle_4_deg18.457
r_dihedral_angle_3_deg12.721
r_dihedral_angle_1_deg5.272
r_long_range_B_refined2.421
r_long_range_B_other2.42
r_angle_refined_deg0.685
r_mcangle_it0.574
r_mcangle_other0.574
r_angle_other_deg0.536
r_scangle_other0.497
r_mcbond_it0.313
r_mcbond_other0.313
r_scbond_it0.276
r_scbond_other0.271
r_chiral_restr0.042
r_bond_refined_d0.003
r_gen_planes_refined0.002
r_bond_other_d
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_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 Atoms85
Heterogen Atoms48

Software

Software
Software NamePurpose
APEXdata collection
PHASERphasing
REFMACrefinement
SAINTdata reduction
APEXdata reduction