8DCW

Lysozyme cluster 0062 (NAG and benzamidine ligands)


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
2.0339.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.78α = 90
b = 78.78β = 90
c = 37.57γ = 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
125097.90.4080.8593.735.0814987
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)
122.121.470.254

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 REPLACEMENTTHROUGHOUT4N8Z239.42791844099.280.190030.187340.23738RANDOM20.413
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]
0.110.11-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.855
r_dihedral_angle_4_deg19.01
r_dihedral_angle_3_deg14.475
r_long_range_B_refined8.67
r_dihedral_angle_1_deg7.494
r_long_range_B_other7.414
r_scangle_other3.616
r_mcangle_other2.227
r_mcangle_it2.198
r_scbond_it2.188
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.855
r_dihedral_angle_4_deg19.01
r_dihedral_angle_3_deg14.475
r_long_range_B_refined8.67
r_dihedral_angle_1_deg7.494
r_long_range_B_other7.414
r_scangle_other3.616
r_mcangle_other2.227
r_mcangle_it2.198
r_scbond_it2.188
r_scbond_other2.186
r_angle_refined_deg1.605
r_mcbond_it1.43
r_angle_other_deg1.379
r_mcbond_other1.309
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms210
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing