7BE0

X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (2)


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
1.9837.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.948α = 90
b = 77.948β = 90
c = 37.38γ = 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-007 HF1.5406

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
11.6226.9998.70.0680.0210.99956.7915018
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)
11.621.6586.60.190.1520.9423.4

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-VALUE193l1.6226.991497773698.6560.1660.16460.202821.371
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]
-0.263-0.2630.525
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.508
r_dihedral_angle_4_deg14.969
r_dihedral_angle_3_deg11.544
r_dihedral_angle_1_deg6.576
r_lrange_it5.829
r_lrange_other5.828
r_scangle_it4.544
r_scangle_other4.542
r_scbond_it3.217
r_scbond_other3.215
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.508
r_dihedral_angle_4_deg14.969
r_dihedral_angle_3_deg11.544
r_dihedral_angle_1_deg6.576
r_lrange_it5.829
r_lrange_other5.828
r_scangle_it4.544
r_scangle_other4.542
r_scbond_it3.217
r_scbond_other3.215
r_mcangle_other2.382
r_mcangle_it2.381
r_angle_refined_deg1.958
r_mcbond_it1.841
r_mcbond_other1.665
r_angle_other_deg1.645
r_symmetry_xyhbond_nbd_refined0.286
r_symmetry_nbd_refined0.282
r_nbd_other0.277
r_xyhbond_nbd_refined0.254
r_nbd_refined0.225
r_symmetry_nbd_other0.215
r_nbtor_refined0.17
r_symmetry_xyhbond_nbd_other0.164
r_ext_dist_refined_d0.104
r_chiral_restr0.101
r_symmetry_nbtor_other0.087
r_metal_ion_refined0.062
r_gen_planes_refined0.02
r_bond_refined_d0.014
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms68

Software

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