X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YS4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529320% PEG 400, 0.1 M HEPES pH 6.5, 0.1 M Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.412α = 90
b = 152.18β = 90
c = 97.762γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-04-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03319APS23-ID-B

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
12.246.7191.50.07720.1675.132719
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)
12.22.2860.60.4672.32148

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 REPLACEMENTTHROUGHOUT1YS42.246.7132667165791.420.2270.2250.279RANDOM48.212
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]
-1.761.360.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.647
r_dihedral_angle_4_deg17.292
r_dihedral_angle_3_deg15.122
r_dihedral_angle_1_deg5.775
r_scangle_it1.631
r_angle_refined_deg1.115
r_scbond_it0.942
r_mcangle_it0.79
r_mcbond_it0.436
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.647
r_dihedral_angle_4_deg17.292
r_dihedral_angle_3_deg15.122
r_dihedral_angle_1_deg5.775
r_scangle_it1.631
r_angle_refined_deg1.115
r_scbond_it0.942
r_mcangle_it0.79
r_mcbond_it0.436
r_nbtor_refined0.295
r_symmetry_vdw_refined0.202
r_nbd_refined0.187
r_symmetry_hbond_refined0.16
r_xyhbond_nbd_refined0.116
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5344
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms48

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction