X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PEL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES4.6293PURE PROTEIN EXTENSIVELY DIALYSED AGAINST SODIUM ACETATE BUFFER AT PH 4.6 WAS USED IN THE CRYSTALLIZATION TRIALS. CRYSTALS WERE OBTAINED BY THE BATCH METHOD USING 4-5 MG/ML PROTEIN IN 0.05 M SODIUM ACETATE BUFFER CONTAINING 0.2 M SODIUM CHLORIDE, 1.5 MM LACTOSE AND 0.05 %SODIUM AZIDE. THE PRECIPITANT USED WAS PEG 8000, A SOLUTION OF WHICH IN THE SAME BUFFER WAS ADDED TO A FINAL CONCENTRATION OF ABOUT 12%. THE TUBES WERE LEFT UNDISTURBED FOR ABOUT TWO WEEKS, BY WHICH TIME CRYSTALS SUITABLE FOR DATA COLLECTION GREW., SMALL TUBES, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.160.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.32α = 90
b = 126.82β = 116.14
c = 85.61γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCHMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.62086.30.1344.756550512.3

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 REPLACEMENTTHROUGHOUT2PEL2.61058584116878.90.2120.2070.272RANDOM21.9
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
x_dihedral_angle_d27.6
x_mcangle_it10.52
x_mcbond_it6.67
x_scangle_it5.72
x_scbond_it4.06
x_angle_deg1.7
x_improper_angle_d1.39
x_bond_d0.01
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d27.6
x_mcangle_it10.52
x_mcbond_it6.67
x_scangle_it5.72
x_scbond_it4.06
x_angle_deg1.7
x_improper_angle_d1.39
x_bond_d0.01
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13944
Nucleic Acid Atoms
Solvent Atoms703
Heterogen Atoms85

Software

Software
Software NamePurpose
AMoREphasing
X-PLORrefinement
XDSdata reduction
DENZOdata reduction
SCALEPACKdata scaling