6GOB

X-ray structure of the adduct formed upon reaction of lysozyme with a Pd(II) complex bearing N,N-pyridylbenzimidazole derivative with an alkylated sulphonate side chain


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.429320% ethylene glycol 0.1 M sodium acetate pH 4.4 0.6 M sodium nitrate
Crystal Properties
Matthews coefficientSolvent content
2.0640.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.487α = 90
b = 79.487β = 90
c = 37.309γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442018-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
11.9656.2199.30.10715.35.98938
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)
11.961.9998.60.5050.7751.53.5

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 REPLACEMENTTHROUGHOUT1DPX1.9656.21848043499.090.172590.169390.23149RANDOM27.259
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]
0.330.33-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.725
r_dihedral_angle_4_deg18.534
r_dihedral_angle_3_deg16.137
r_dihedral_angle_1_deg6.194
r_long_range_B_refined5.822
r_long_range_B_other5.819
r_scangle_other4.057
r_scbond_it2.623
r_scbond_other2.499
r_mcangle_it2.355
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.725
r_dihedral_angle_4_deg18.534
r_dihedral_angle_3_deg16.137
r_dihedral_angle_1_deg6.194
r_long_range_B_refined5.822
r_long_range_B_other5.819
r_scangle_other4.057
r_scbond_it2.623
r_scbond_other2.499
r_mcangle_it2.355
r_mcangle_other2.346
r_angle_refined_deg2.215
r_angle_other_deg1.862
r_mcbond_it1.684
r_mcbond_other1.684
r_chiral_restr0.09
r_gen_planes_refined0.048
r_bond_refined_d0.016
r_bond_other_d0.01
r_gen_planes_other0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms141

Software

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