7BEC

Unusual structural features in the adduct of dirhodium tetraacetate with lysozyme (5)


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, 0.1 M sodium nitrate
Crystal Properties
Matthews coefficientSolvent content
2.0138.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.7α = 90
b = 78.7β = 90
c = 37.245γ = 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
11.7435.1991.10.070.02124.72511349
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)
11.741.83363.120.8480.4741.127.6

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-VALUE193L1.7435.191134955590.7560.1870.18470.228442.938
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]
-0.227-0.2270.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.207
r_dihedral_angle_4_deg18.595
r_dihedral_angle_3_deg14.871
r_lrange_other9.528
r_lrange_it9.527
r_dihedral_angle_1_deg7.122
r_scangle_it7.037
r_scangle_other7.032
r_scbond_it4.462
r_scbond_other4.459
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.207
r_dihedral_angle_4_deg18.595
r_dihedral_angle_3_deg14.871
r_lrange_other9.528
r_lrange_it9.527
r_dihedral_angle_1_deg7.122
r_scangle_it7.037
r_scangle_other7.032
r_scbond_it4.462
r_scbond_other4.459
r_mcangle_other3.977
r_mcangle_it3.969
r_mcbond_it3.025
r_mcbond_other3.006
r_angle_refined_deg1.553
r_angle_other_deg1.384
r_xyhbond_nbd_refined0.228
r_nbd_refined0.222
r_nbd_other0.194
r_symmetry_nbd_other0.191
r_ext_dist_refined_d0.19
r_symmetry_xyhbond_nbd_refined0.171
r_symmetry_nbd_refined0.166
r_nbtor_refined0.159
r_metal_ion_refined0.093
r_symmetry_nbtor_other0.081
r_chiral_restr0.079
r_xyhbond_nbd_other0.025
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MOSFLMdata scaling
PHASERphasing