5IDD

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 4OXE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE4.7293CRYSTALLIZATION CONDITIONS: 40MG HEWL (2.7MM) CO-CRYSTALLISED WITH 3MG CARBOPLATIN (8.1MM). 462.5 microL OF A 0.02M NAAC SOLUTION ALONG REMARK 280 WITH 462.5 microL OF A 0.5M NANO3 SOLUTION WAS USED WITH 75 microL DMSO.
Crystal Properties
Matthews coefficientSolvent content
1.7931.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 26.957α = 88.76
b = 31.794β = 71.99
c = 34.055γ = 68.33
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDAPEX II CCDCONFOCAL MIRROR OPTICS2012-11-18MSINGLE 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
11.1332.2194.10.0867.22.935817
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)
11.131.16770.3121.1

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 REPLACEMENTTHROUGHOUT4oxe1.1332.2133282176294.090.179640.17750.21982RANDOM12.268
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.443
r_sphericity_free27.301
r_dihedral_angle_4_deg19.942
r_sphericity_bonded11.116
r_dihedral_angle_3_deg10.158
r_rigid_bond_restr8.793
r_dihedral_angle_1_deg6.948
r_scangle_other4.131
r_long_range_B_refined3.87
r_long_range_B_other3.869
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.443
r_sphericity_free27.301
r_dihedral_angle_4_deg19.942
r_sphericity_bonded11.116
r_dihedral_angle_3_deg10.158
r_rigid_bond_restr8.793
r_dihedral_angle_1_deg6.948
r_scangle_other4.131
r_long_range_B_refined3.87
r_long_range_B_other3.869
r_scbond_it3.526
r_scbond_other3.523
r_mcangle_other2.77
r_mcangle_it2.602
r_mcbond_it2.096
r_angle_refined_deg2.056
r_mcbond_other1.869
r_angle_other_deg1.044
r_chiral_restr0.149
r_bond_refined_d0.021
r_gen_planes_refined0.012
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 Atoms986
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
APEX 2data scaling
PHASERphasing