6ZZ2

Cocktail experiment E: fragments 52, 58, and 63 at 90 mM concentration in complex with Endothiapepsin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DQ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2900.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystals obtained by streak-seeding
Crystal Properties
Matthews coefficientSolvent content
1.935.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.401α = 90
b = 73.178β = 109.762
c = 52.659γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.14841.03499.50.99913.93.711466110.2714223387
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.151.220.768

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5DQ41.1488543913141.03349661081.36387254305114654573399.6280912740.1274915962490.1265902054090.14455125856813.9693194313
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
f_dihedral_angle_d14.5161168647
f_angle_d1.01969804243
f_chiral_restr0.082051223726
f_plane_restr0.00760725295564
f_bond_d0.00735224508321
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2372
Nucleic Acid Atoms
Solvent Atoms315
Heterogen Atoms37

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
XSCALEdata scaling
PHASERphasing
XDSdata reduction