7BEB

Unusual structural features in the adduct of dirhodium tetraacetate with lysozyme (4)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 193L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52930.1 M sodium acetate, 20% ethylene glicol, 0.6 M sodium nitrate
Crystal Properties
Matthews coefficientSolvent content
2.0138.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.604α = 90
b = 78.604β = 90
c = 37.307γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.3255.5895.40.0470.013128.825.826513
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.321.3751.12.550.720.61225.9

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-VALUE193l1.3255.5826513128695.3840.180.17770.223327.339
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]
-0.011-0.0110.022
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.632
r_dihedral_angle_4_deg19.989
r_dihedral_angle_3_deg12.66
r_lrange_it7.461
r_lrange_other7.329
r_dihedral_angle_1_deg6.438
r_scangle_it5.514
r_scangle_other5.511
r_scbond_it3.704
r_scbond_other3.704
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.632
r_dihedral_angle_4_deg19.989
r_dihedral_angle_3_deg12.66
r_lrange_it7.461
r_lrange_other7.329
r_dihedral_angle_1_deg6.438
r_scangle_it5.514
r_scangle_other5.511
r_scbond_it3.704
r_scbond_other3.704
r_mcangle_other2.672
r_mcangle_it2.66
r_angle_refined_deg2.394
r_mcbond_it2.324
r_mcbond_other1.978
r_angle_other_deg1.643
r_nbd_refined0.252
r_nbd_other0.248
r_ext_dist_refined_d0.247
r_symmetry_xyhbond_nbd_refined0.242
r_xyhbond_nbd_refined0.221
r_symmetry_nbd_other0.214
r_xyhbond_nbd_other0.201
r_nbtor_refined0.173
r_symmetry_nbd_refined0.156
r_symmetry_xyhbond_nbd_other0.136
r_metal_ion_refined0.104
r_chiral_restr0.097
r_symmetry_nbtor_other0.088
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_bond_other_d0.009
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MOSFLMdata scaling
PHASERphasing