5HQ1

Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamics of cisplatin binding to histidine in a protein Struct. Dyn. 1, 034701 (2014) regarding the refinement of 4mwk, 4mwm, 4mwn and 4oxe and the method we have adopted.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.7294CRYSTALLIZATION CONDITIONS: 40MG HEWL CO-CRYSTALLISED WITH 2.6MG CISPLATIN, WITH THE PLATINUM COMPOUNDS BEING IN A 3-FOLD MOLAR EXCESS TO THE PROTEIN. 462.5 UL OF A 0.02M NAAC SOLUTION ALONG WITH 462.5 UL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 UL DMSO ADDED, BATCH, TEMPERATURE 294K, PH 4.7, EVAPORATION.
Crystal Properties
Matthews coefficientSolvent content
1.7429.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 26.777α = 88.9
b = 31.382β = 72.31
c = 33.865γ = 68.46
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDAPEX II CCD2012-11-03MSINGLE 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
1132.0990.80.08755.932.25476957.4
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)
111.179.70.24081.330.81

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4mwm132.0945284241090.80.173170.171880.19699RANDOM11.704
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]
0.380.14-0.87-0.270.54-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.027
r_sphericity_free27.127
r_dihedral_angle_4_deg16.472
r_sphericity_bonded12.287
r_dihedral_angle_3_deg10.297
r_dihedral_angle_1_deg6.963
r_rigid_bond_restr6.1
r_scangle_other4.517
r_scbond_other3.804
r_scbond_it3.773
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.027
r_sphericity_free27.127
r_dihedral_angle_4_deg16.472
r_sphericity_bonded12.287
r_dihedral_angle_3_deg10.297
r_dihedral_angle_1_deg6.963
r_rigid_bond_restr6.1
r_scangle_other4.517
r_scbond_other3.804
r_scbond_it3.773
r_long_range_B_refined3.606
r_long_range_B_other3.532
r_mcangle_it2.31
r_mcangle_other2.308
r_mcbond_other1.922
r_mcbond_it1.921
r_angle_refined_deg1.908
r_angle_other_deg0.977
r_chiral_restr0.139
r_bond_refined_d0.023
r_gen_planes_refined0.01
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms976
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
APEXdata scaling
PHASERphasing