X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E61PDB entry 3E61

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M Na HEPES, 5% Isopropanol, 20% PEG 2000 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.709α = 90
b = 70.709β = 90
c = 222.823γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmSagitally focused second crystal, vertical focusing via a one-meter, Pt/Pd-coated cylindrically focusing mirror2008-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-BM1.000APS17-BM

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
12.75095.40.10417.0716.7284952849351.075
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)
2.72.893.40.4576.32034

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 3E612.731.3127040144295.490.216090.212450.28261RANDOM28.748
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
r_dihedral_angle_2_deg38.537
r_dihedral_angle_4_deg24.048
r_dihedral_angle_3_deg21.783
r_dihedral_angle_1_deg7.517
r_scangle_it2.797
r_angle_refined_deg1.909
r_scbond_it1.828
r_mcangle_it1.172
r_mcbond_it0.677
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.537
r_dihedral_angle_4_deg24.048
r_dihedral_angle_3_deg21.783
r_dihedral_angle_1_deg7.517
r_scangle_it2.797
r_angle_refined_deg1.909
r_scbond_it1.828
r_mcangle_it1.172
r_mcbond_it0.677
r_nbtor_refined0.315
r_nbd_refined0.236
r_symmetry_vdw_refined0.206
r_xyhbond_nbd_refined0.185
r_chiral_restr0.136
r_bond_refined_d0.019
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7530
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms120

Software

Software
Software NamePurpose
MAR345data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling