7BE1

X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (3)


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
2.0138.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.36α = 90
b = 78.36β = 90
c = 37.61γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-06-02MSINGLE 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
11.478.361000.0990.0230.99910.219.623665
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)
11.41.4710020.5190.70116.6

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-VALUE193L1.455.40923665121299.970.1910.19010.208916.827
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]
-0.347-0.3470.694
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.339
r_dihedral_angle_3_deg14.973
r_dihedral_angle_4_deg14.543
r_lrange_it6.85
r_lrange_other6.653
r_dihedral_angle_1_deg6.515
r_scangle_it4.249
r_scangle_other4.247
r_scbond_it2.801
r_scbond_other2.798
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.339
r_dihedral_angle_3_deg14.973
r_dihedral_angle_4_deg14.543
r_lrange_it6.85
r_lrange_other6.653
r_dihedral_angle_1_deg6.515
r_scangle_it4.249
r_scangle_other4.247
r_scbond_it2.801
r_scbond_other2.798
r_mcangle_other2.168
r_mcangle_it2.162
r_angle_refined_deg1.866
r_angle_other_deg1.644
r_mcbond_it1.556
r_mcbond_other1.466
r_nbd_other0.27
r_nbd_refined0.252
r_ext_dist_refined_d0.24
r_xyhbond_nbd_refined0.239
r_symmetry_nbd_other0.209
r_symmetry_xyhbond_nbd_refined0.194
r_nbtor_refined0.171
r_symmetry_nbd_refined0.158
r_chiral_restr0.102
r_metal_ion_refined0.097
r_symmetry_nbtor_other0.088
r_symmetry_xyhbond_nbd_other0.074
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_bond_other_d0.008
r_xyhbond_nbd_other0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
MOSFLMdata scaling
PHASERphasing