2H9J

Structure of Hen egg white lysozyme soaked with Ni2-Xylylbicyclam


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.5277Acetate buffer, NaCl , pH 4.5, VAPOR DIFFUSION, temperature 277K, temperature 277.0K
Crystal Properties
Matthews coefficientSolvent content
2.0138.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.577α = 90
b = 77.577β = 90
c = 38.355γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.11.488SRSPX14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7534.3899.911704

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1YIL1.7534.38123291170458799.90.1840.186590.1840.23214RANDOM25.685
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.85
r_dihedral_angle_4_deg19.865
r_dihedral_angle_3_deg13.096
r_dihedral_angle_1_deg6.087
r_scangle_it4.437
r_scbond_it2.937
r_mcangle_it1.952
r_angle_refined_deg1.795
r_mcbond_it1.11
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.85
r_dihedral_angle_4_deg19.865
r_dihedral_angle_3_deg13.096
r_dihedral_angle_1_deg6.087
r_scangle_it4.437
r_scbond_it2.937
r_mcangle_it1.952
r_angle_refined_deg1.795
r_mcbond_it1.11
r_nbtor_refined0.295
r_symmetry_hbond_refined0.215
r_symmetry_vdw_refined0.211
r_nbd_refined0.211
r_xyhbond_nbd_refined0.183
r_metal_ion_refined0.158
r_chiral_restr0.12
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_metal_ion_other
r_nbd_other
r_symmetry_vdw_other
r_angle_other_deg
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbtor_other
r_mcbond_other
r_gen_planes_other
r_bond_other_d
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1007
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement