6MX9

Lysozyme bound to 3-Aminophenol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4N8Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629310uL of 50mM 3-aminophenol was deposited on a cover slip and allowed to dry. A 20 uL pellet of 4% sodium chloride + 5% ethylene glycol + 10% glycerol in 2% agar was deposited on the cover slip. Adjacent to this was positioned lysozyme (10 ul of 30 mg/ml lysozyme in 100 mM sodium acetate pH 4.6). The cover slip was equilibrated over precipitant containing all the crystallization components.
Crystal Properties
Matthews coefficientSolvent content
2.0840.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.085α = 90
b = 80.085β = 90
c = 37.197γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.9202NSLS-II17-ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.3528.3199.70.0680.99821.912.825655
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.39960.7250.9063.211.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4N8Z1.3528.3125655135999.670.158980.157540.1859RANDOM18.817
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_deg35.789
r_dihedral_angle_4_deg21.61
r_dihedral_angle_3_deg13.121
r_long_range_B_refined7.025
r_long_range_B_other6.982
r_dihedral_angle_1_deg6.426
r_scangle_other4.437
r_scbond_other2.977
r_scbond_it2.976
r_angle_refined_deg2.533
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.789
r_dihedral_angle_4_deg21.61
r_dihedral_angle_3_deg13.121
r_long_range_B_refined7.025
r_long_range_B_other6.982
r_dihedral_angle_1_deg6.426
r_scangle_other4.437
r_scbond_other2.977
r_scbond_it2.976
r_angle_refined_deg2.533
r_mcangle_other2.169
r_mcangle_it2.152
r_mcbond_it1.54
r_mcbond_other1.474
r_angle_other_deg1.276
r_chiral_restr0.171
r_bond_refined_d0.029
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1001
Nucleic Acid Atoms
Solvent Atoms218
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing