4XPU

The crystal structure of EndoV from E.coli


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529826% PEG 3350, 0.05M sodium fluoride, 0.1M MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.2745.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.892α = 90
b = 84.783β = 90
c = 91.507γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180CCDOXFORD ONYX CCDOnyx2014-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOXFORD DIFFRACTION ENHANCE ULTRA1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.462.299.50.1579.54.717499
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5399.90.6692.54.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4NSP2.462.191658188799.230.197910.194840.20.255120.26RANDOM27.212
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]
-0.54-0.420.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.427
r_dihedral_angle_3_deg19.203
r_dihedral_angle_4_deg19.03
r_dihedral_angle_1_deg6.393
r_long_range_B_refined5.49
r_long_range_B_other5.434
r_scangle_other3.242
r_mcangle_it2.663
r_mcangle_other2.662
r_scbond_it1.948
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3242
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing