8DCV

Lysozyme cluster 0043, NAG ligand


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62904% SODIUM CHLORIDE, 100MM SODIUM ACETATE PH 4.6, 120MG/ML
Crystal Properties
Matthews coefficientSolvent content
2.0239.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.46α = 90
b = 78.46β = 90
c = 37.69γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2016-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-10.92NSLS-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
125099.90.2810.9767.219.915237
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)
122.120.7470.804

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 REPLACEMENTTHROUGHOUT4N8Z239.26795043399.980.14920.147120.18683RANDOM20.465
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]
0.040.04-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.874
r_dihedral_angle_4_deg20.984
r_dihedral_angle_3_deg13.602
r_long_range_B_refined12.27
r_long_range_B_other11.289
r_dihedral_angle_1_deg7.376
r_scangle_other4.936
r_scbond_it3.13
r_scbond_other3.128
r_mcangle_other2.813
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.874
r_dihedral_angle_4_deg20.984
r_dihedral_angle_3_deg13.602
r_long_range_B_refined12.27
r_long_range_B_other11.289
r_dihedral_angle_1_deg7.376
r_scangle_other4.936
r_scbond_it3.13
r_scbond_other3.128
r_mcangle_other2.813
r_mcangle_it2.747
r_angle_refined_deg1.855
r_mcbond_it1.766
r_mcbond_other1.603
r_angle_other_deg1.462
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms213
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing