X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION629510% PEG 4000, 100mM MES pH 6.0, VAPOR DIFFUSION, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5752.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 230.625α = 90
b = 99.88β = 103.12
c = 62.9γ = 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 X06DA0.9999SLSX06DA

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
12.4848.898.30.0470.04714.823.347564485522220.736
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)
12.482.5796.20.6570.6573.013.24849

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2B8L2.4848.82248570475649861000.227030.2260.225850.28115RANDOM20.736
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]
-7.7-0.13-5.1312.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.663
r_dihedral_angle_4_deg20.226
r_dihedral_angle_3_deg15.73
r_dihedral_angle_1_deg6.727
r_scangle_it2.145
r_scbond_it1.45
r_angle_refined_deg1.21
r_angle_other_deg1.17
r_mcangle_it1.075
r_mcbond_it0.869
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.663
r_dihedral_angle_4_deg20.226
r_dihedral_angle_3_deg15.73
r_dihedral_angle_1_deg6.727
r_scangle_it2.145
r_scbond_it1.45
r_angle_refined_deg1.21
r_angle_other_deg1.17
r_mcangle_it1.075
r_mcbond_it0.869
r_symmetry_vdw_other0.281
r_nbd_other0.192
r_symmetry_vdw_refined0.191
r_nbd_refined0.189
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.156
r_symmetry_hbond_refined0.104
r_mcbond_other0.093
r_nbtor_other0.083
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_xyhbond_nbd_other0.004
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8784
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms54

Software

Software
Software NamePurpose
SLSPXdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling