X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YFXPDB ENTRY 2YFX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.4286CRYSTALS WERE GROWN AT 13 DEGREE CELSIUS BY VAPOR DIFFUSION AFTER MIXING 2 MICROLITERS OF PROTEIN SOLUTION WITH 2 MICROLITERS OF A RESERVOIR SOLUITON CONTAINING: 0.1 M TRIS PH 8.4, 0.2 M LITHIUM SULFATE, 0.1% (W/V) B-OCTYLGLUCOSIDE, AND 20% (W/V) PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.2745.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.101α = 90
b = 57.76β = 90
c = 105.19γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102010-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-IDAPS17-ID

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
11.89105.1999.80.0618.76.425946122.2
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)
11.89299.90.473.96.7

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2YFX1.952.62565774199.70.2060.2060.238RANDOM31.2
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]
-4.73-2.26.93
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.9
c_scangle_it3.69
c_scbond_it2.45
c_mcangle_it2.31
c_mcbond_it1.48
c_angle_deg0.8
c_improper_angle_d0.67
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.9
c_scangle_it3.69
c_scbond_it2.45
c_mcangle_it2.31
c_mcbond_it1.48
c_angle_deg0.8
c_improper_angle_d0.67
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2296
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
autoPROCdata reduction
SCALAdata scaling
CNXphasing