4YEN

Room temperature X-ray diffraction studies of cisplatin binding to HEWL in DMSO media after 14 months of crystal storage - new refinement


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4G4A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.7295HEWL co-crystallized with cisplatin with 5% DMSO media in 1 mL 10% sodium chloride + 1 ml 0.04 M sodium acetate, pH 4.7
Crystal Properties
Matthews coefficientSolvent content
2.0740.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.113α = 90
b = 79.113β = 90
c = 37.985γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295CCDAPEX II CCD2012-01-25MSINGLE 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)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12501000.0860.0860.0920.0328.87.986028602-325.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.031000.5710.630.2640.8652.75.6411

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4G4A250810745099.80.14810.14640.1788RANDOM28.046
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]
0.060.06-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.32
r_sphericity_bonded30.527
r_sphericity_free25.995
r_dihedral_angle_4_deg23.506
r_dihedral_angle_3_deg14.34
r_dihedral_angle_1_deg6.307
r_angle_refined_deg1.578
r_mcangle_it1.54
r_angle_other_deg1.069
r_mcbond_it0.906
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.32
r_sphericity_bonded30.527
r_sphericity_free25.995
r_dihedral_angle_4_deg23.506
r_dihedral_angle_3_deg14.34
r_dihedral_angle_1_deg6.307
r_angle_refined_deg1.578
r_mcangle_it1.54
r_angle_other_deg1.069
r_mcbond_it0.906
r_mcbond_other0.905
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms995
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
APEXdata collection
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building
PDB_EXTRACTdata extraction
PHASERphasing