6ZS8

X-ray structure of the adduct formed upon treating lysozyme with an aged solution of arsenoplatin-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4J1A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429820% ethylene glycol 0.1 M sodium acetate pH 4.0 0.6 M sodium nitrate
Crystal Properties
Matthews coefficientSolvent content
1.8633.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.703α = 90
b = 78.703β = 90
c = 34.462γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442015-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.1555.6599.50.11385.76242
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)
12.152.191000.6395.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4J1A2.15325.939622128999.6320.1870.18470.238932.612
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]
-0.658-0.6581.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.613
r_dihedral_angle_4_deg20.072
r_dihedral_angle_3_deg17.939
r_dihedral_angle_1_deg7.917
r_lrange_it7.114
r_lrange_other7.112
r_scangle_it4.249
r_scangle_other4.247
r_mcangle_it3.674
r_mcangle_other3.672
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.613
r_dihedral_angle_4_deg20.072
r_dihedral_angle_3_deg17.939
r_dihedral_angle_1_deg7.917
r_lrange_it7.114
r_lrange_other7.112
r_scangle_it4.249
r_scangle_other4.247
r_mcangle_it3.674
r_mcangle_other3.672
r_scbond_it2.724
r_scbond_other2.722
r_mcbond_other2.302
r_mcbond_it2.301
r_angle_refined_deg1.696
r_angle_other_deg1.322
r_nbd_other0.277
r_metal_ion_refined0.27
r_symmetry_nbd_refined0.26
r_nbd_refined0.234
r_symmetry_nbd_other0.211
r_symmetry_xyhbond_nbd_refined0.188
r_nbtor_refined0.16
r_xyhbond_nbd_refined0.155
r_symmetry_nbtor_other0.08
r_chiral_restr0.071
r_ext_dist_refined_d0.063
r_xyhbond_nbd_other0.053
r_gen_planes_refined0.01
r_bond_refined_d0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing