2DQA

Crystal Structure of Tapes japonica Lysozyme


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52950.8M sodium citrate, 0.8M ammonium sulfate, 0.5mM beta-heptyl thioglucoside, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6553.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.749α = 90
b = 88.76β = 116.04
c = 43.644γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102004-12-04MSINGLE WAVELENGTH
21x-ray100CCDBRUKER SMART 60002004-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B10.97904SPring-8BL38B1
2ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
1,21.65094.80.0620.0559.43.5383903641163.8
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)
1,21.61.6678.40.3080.272.32.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUT1.633.863638434538183694.820.17640.174680.20994RANDOM22.18
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.029
r_dihedral_angle_4_deg12.17
r_dihedral_angle_3_deg11.822
r_sphericity_free6.712
r_dihedral_angle_1_deg4.887
r_scangle_it1.895
r_scbond_it1.169
r_angle_refined_deg1.082
r_mcangle_it0.856
r_mcbond_it0.516
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.029
r_dihedral_angle_4_deg12.17
r_dihedral_angle_3_deg11.822
r_sphericity_free6.712
r_dihedral_angle_1_deg4.887
r_scangle_it1.895
r_scbond_it1.169
r_angle_refined_deg1.082
r_mcangle_it0.856
r_mcbond_it0.516
r_nbtor_refined0.3
r_metal_ion_refined0.198
r_nbd_refined0.19
r_symmetry_vdw_refined0.183
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.093
r_chiral_restr0.077
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1908
Nucleic Acid Atoms
Solvent Atoms354
Heterogen Atoms118

Software

Software
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
SOLVEphasing
CNSrefinement
CrystalCleardata reduction
HKL-2000data scaling
REFMACrefinement