2HUB

Structure of Hen Egg-White Lysozyme Determined from crystals grown in pH 7.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIn-house structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Microbatch, Douglas Instrument robot7.52930.1 M HEPES-Na pH 7.5, 0.8M Potassium Sodium Tartrate tetrahydrate, Microbatch, Douglas Instrument robot, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8533.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.861α = 90
b = 76.861β = 90
c = 35.867γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Mirrors2005-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9737ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
11.20154.3198.20.0540.05416.86.23358733587-310.95
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.2011.2274.30.4750.4192.12.71242

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUTIn-house structure1.20154.31-33353833538168898.380.1380.1380.1370.173RANDOM11.052
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]
-1.12-1.122.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.808
r_dihedral_angle_4_deg23.904
r_sphericity_free14.246
r_dihedral_angle_3_deg11.511
r_sphericity_bonded8.756
r_scangle_it6.77
r_dihedral_angle_1_deg5.976
r_scbond_it5.48
r_mcangle_it4.055
r_mcbond_other3.411
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.808
r_dihedral_angle_4_deg23.904
r_sphericity_free14.246
r_dihedral_angle_3_deg11.511
r_sphericity_bonded8.756
r_scangle_it6.77
r_dihedral_angle_1_deg5.976
r_scbond_it5.48
r_mcangle_it4.055
r_mcbond_other3.411
r_mcbond_it3.298
r_rigid_bond_restr3.015
r_angle_refined_deg1.697
r_angle_other_deg1.185
r_symmetry_vdw_other0.291
r_xyhbond_nbd_refined0.263
r_nbd_refined0.25
r_symmetry_hbond_refined0.218
r_nbd_other0.215
r_symmetry_vdw_refined0.188
r_nbtor_refined0.185
r_chiral_restr0.11
r_nbtor_other0.089
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1069
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing