6ZSQ

Crystal structure of the Cisplatin beta-Lactoglobulin adduct formed after 18 h of soaking


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BEB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.9293Crystals of beta-Lactoglobulin were grown using 3.0 M (NH4)2SO4, 0.1 M sodium/potassium phosphate buffer pH 6.9 as reservoir. Protein crystallizes at a concentration of 18 mg/mL. Crystals of beta-Lactoglobulin were soaked in a solution consisting of 3.0 M (NH4)2SO4, 0.1 M sodium/potassium phosphate buffer (pH 6.9) with 5 mM CDDP (about 1:3 protein to metal ratio).
Crystal Properties
Matthews coefficientSolvent content
2.1643.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.72α = 69.96
b = 49.05β = 68.59
c = 49.31γ = 77
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442018-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
1223.2386.90.060.9588.82.317918
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0692.40.1520.9393.91.9

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-VALUE1BEB2.00423.2281791889486.8740.1850.18270.224122.264
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]
0.2330.2860.182-0.0561.7070.611
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.838
r_dihedral_angle_3_deg18.598
r_dihedral_angle_4_deg16.465
r_lrange_it9.099
r_lrange_other9.093
r_dihedral_angle_1_deg6.959
r_scangle_it4.046
r_scangle_other3.99
r_mcangle_other3.522
r_mcangle_it3.521
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.838
r_dihedral_angle_3_deg18.598
r_dihedral_angle_4_deg16.465
r_lrange_it9.099
r_lrange_other9.093
r_dihedral_angle_1_deg6.959
r_scangle_it4.046
r_scangle_other3.99
r_mcangle_other3.522
r_mcangle_it3.521
r_scbond_it2.469
r_scbond_other2.439
r_mcbond_it2.093
r_mcbond_other2.092
r_angle_refined_deg1.616
r_angle_other_deg1.246
r_ext_dist_refined_d0.3
r_nbd_other0.218
r_nbd_refined0.205
r_symmetry_nbd_other0.202
r_xyhbond_nbd_refined0.174
r_symmetry_xyhbond_nbd_refined0.166
r_nbtor_refined0.154
r_symmetry_nbd_refined0.136
r_symmetry_nbtor_other0.082
r_chiral_restr0.073
r_symmetry_xyhbond_nbd_other0.058
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2556
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing