7BE2

X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (6)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.01 M HEPES, 2.00 M sodium formate
Crystal Properties
Matthews coefficientSolvent content
2.0239.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.93α = 90
b = 78.93β = 90
c = 37.12γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1.5406ELETTRA11.2C

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
11.6555.812940.120.025122.524.511800
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)
11.651.852.63.230.680.511.322.4

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-VALUE193L1.6555.811180059580.6010.1850.18190.234130.659
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]
-0.023-0.0230.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.069
r_dihedral_angle_4_deg23.303
r_dihedral_angle_3_deg14.523
r_lrange_it8.384
r_lrange_other8.349
r_dihedral_angle_1_deg7.409
r_scangle_it5.727
r_scangle_other5.723
r_mcangle_it3.551
r_mcangle_other3.551
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.069
r_dihedral_angle_4_deg23.303
r_dihedral_angle_3_deg14.523
r_lrange_it8.384
r_lrange_other8.349
r_dihedral_angle_1_deg7.409
r_scangle_it5.727
r_scangle_other5.723
r_mcangle_it3.551
r_mcangle_other3.551
r_scbond_it3.522
r_scbond_other3.52
r_mcbond_it2.475
r_mcbond_other2.456
r_angle_refined_deg1.546
r_angle_other_deg1.411
r_nbd_refined0.218
r_symmetry_xyhbond_nbd_refined0.201
r_nbd_other0.199
r_symmetry_nbd_other0.194
r_xyhbond_nbd_refined0.172
r_nbtor_refined0.162
r_metal_ion_refined0.147
r_symmetry_nbd_refined0.112
r_chiral_restr0.079
r_symmetry_nbtor_other0.078
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 Atoms1001
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MOSFLMdata scaling
PHASERphasing