7BDZ

X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (1)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52930.1M sodium acetate, 20% ethylene glicol, 0.6 M sodium nitrate
Crystal Properties
Matthews coefficientSolvent content
1.9837.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.964α = 90
b = 77.964β = 90
c = 37.291γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442016-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
11.9425.48990.0950.0450.99714.95.38895
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)
11.941.970.440.2490.8082.2

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-VALUE193l1.9425.48887543099.1620.1590.15620.217421.212
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]
-0.299-0.2990.598
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.34
r_dihedral_angle_4_deg16.344
r_dihedral_angle_3_deg12.039
r_dihedral_angle_1_deg6.989
r_lrange_it5.886
r_lrange_other5.884
r_scangle_it3.896
r_scangle_other3.894
r_scbond_it2.526
r_scbond_other2.524
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.34
r_dihedral_angle_4_deg16.344
r_dihedral_angle_3_deg12.039
r_dihedral_angle_1_deg6.989
r_lrange_it5.886
r_lrange_other5.884
r_scangle_it3.896
r_scangle_other3.894
r_scbond_it2.526
r_scbond_other2.524
r_angle_refined_deg2.384
r_mcangle_it2.088
r_mcangle_other2.085
r_mcbond_it1.576
r_angle_other_deg1.51
r_mcbond_other1.443
r_nbd_other0.309
r_symmetry_xyhbond_nbd_refined0.255
r_xyhbond_nbd_refined0.24
r_nbd_refined0.224
r_symmetry_nbd_other0.21
r_symmetry_nbd_refined0.189
r_nbtor_refined0.161
r_symmetry_xyhbond_nbd_other0.145
r_ext_dist_refined_d0.13
r_chiral_restr0.091
r_symmetry_nbtor_other0.084
r_metal_ion_refined0.073
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms76

Software

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