X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B8LPDB ENTRY 2B8L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION629310% PEG 4000, 100mM MES pH 6.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6753.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 232.55α = 90
b = 100.13β = 103.73
c = 64.78γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-01-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.2548.3497.20.0450.04513.26366620664282229.654
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.4489.90.3470.3472.652.313253

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)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 2B8L2.2648.3422666206311033181000.224560.222450.26487RANDOM29.654
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]
-5.87-1.19-1.466.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.067
r_dihedral_angle_4_deg19.241
r_dihedral_angle_3_deg14.154
r_dihedral_angle_1_deg6.725
r_scangle_it1.734
r_scbond_it1.221
r_angle_refined_deg1.154
r_mcangle_it0.918
r_angle_other_deg0.732
r_mcbond_it0.719
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.067
r_dihedral_angle_4_deg19.241
r_dihedral_angle_3_deg14.154
r_dihedral_angle_1_deg6.725
r_scangle_it1.734
r_scbond_it1.221
r_angle_refined_deg1.154
r_mcangle_it0.918
r_angle_other_deg0.732
r_mcbond_it0.719
r_symmetry_vdw_refined0.269
r_symmetry_vdw_other0.209
r_nbd_refined0.181
r_nbtor_refined0.178
r_nbd_other0.169
r_xyhbond_nbd_refined0.154
r_mcbond_other0.118
r_xyhbond_nbd_other0.117
r_symmetry_hbond_refined0.102
r_nbtor_other0.08
r_chiral_restr0.068
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8830
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms39

Software

Software
Software NamePurpose
SLSPXdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling