4G4B

Room temperature X-ray diffraction study of cisplatin binding to HEWL in DMSO media with NAG after 7 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 cisplatin and NAG in 7.5% DMSO media in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7, BATCH, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0640.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.822α = 90
b = 78.822β = 90
c = 38.019γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295CCDAPEX II CCD2012-01-24MSINGLE 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
12.155.73652.60.17716.119.213385705542
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)
12.12.131000.7495.113.2

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2W1Y2.155.7362413385705034399.990.162330.159270.22701RANDOM24.044
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]
-0.1-0.10.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.27
r_dihedral_angle_4_deg25.586
r_dihedral_angle_3_deg15.313
r_dihedral_angle_1_deg7.096
r_angle_refined_deg2.531
r_angle_other_deg1.07
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.27
r_dihedral_angle_4_deg25.586
r_dihedral_angle_3_deg15.313
r_dihedral_angle_1_deg7.096
r_angle_refined_deg2.531
r_angle_other_deg1.07
r_chiral_restr0.118
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
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 Atoms35
Heterogen Atoms29

Software

Software
Software NamePurpose
APEXdata collection
PHASERphasing
REFMACrefinement
EVAL15data reduction
EVAL15data scaling