2HU3

Parent Structure of Hen Egg White Lysozyme grown in acidic pH 4.8. Refinement for comparison with crosslinked molecules of lysozyme


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.82930.1M Na Acetate, pH 4.8, 7% NaCl, 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
238.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.87α = 90
b = 78.87β = 90
c = 36.788γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2005-06-15MSINGLE 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
11.355.731000.0570.05710.5272916129161-310.43
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)
11.31.321000.5380.523.9215.91416

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTIn-house model1.355.73-32911129111147799.980.1050.1050.1030.145RANDOM10.981
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]
0.090.09-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.179
r_dihedral_angle_4_deg19.117
r_sphericity_free17.031
r_dihedral_angle_3_deg11.707
r_scangle_it8.325
r_sphericity_bonded7.057
r_scbond_it6.984
r_dihedral_angle_1_deg5.873
r_mcangle_it4.52
r_mcbond_it3.603
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.179
r_dihedral_angle_4_deg19.117
r_sphericity_free17.031
r_dihedral_angle_3_deg11.707
r_scangle_it8.325
r_sphericity_bonded7.057
r_scbond_it6.984
r_dihedral_angle_1_deg5.873
r_mcangle_it4.52
r_mcbond_it3.603
r_rigid_bond_restr3.475
r_mcbond_other2.723
r_angle_refined_deg1.571
r_angle_other_deg1.141
r_symmetry_vdw_other0.363
r_nbd_refined0.268
r_symmetry_vdw_refined0.256
r_nbd_other0.23
r_xyhbond_nbd_refined0.214
r_metal_ion_refined0.206
r_symmetry_hbond_refined0.189
r_nbtor_refined0.186
r_chiral_restr0.122
r_nbtor_other0.085
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms39

Software

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