X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DIJPDB ENTRY 4DIJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82982.4M AmSO4, 0.1M Tris, 0.1M NaCitrate, pH 8.0, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1442.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.814α = 90
b = 165.528β = 95.06
c = 34.236γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.00146SLSX10SA

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
12.32097.80.11910.96.11653416534
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)
12.3022.3897.30.1572.91672

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 4DIJ2.320162661626682498.270.19590.19590.19440.2243RANDOM13.29
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]
0.680.26-0.840.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.737
r_dihedral_angle_4_deg20.842
r_dihedral_angle_3_deg15.9
r_dihedral_angle_1_deg5.62
r_scangle_it1.942
r_scbond_it1.223
r_angle_refined_deg1.184
r_mcangle_it0.833
r_mcbond_it0.496
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.737
r_dihedral_angle_4_deg20.842
r_dihedral_angle_3_deg15.9
r_dihedral_angle_1_deg5.62
r_scangle_it1.942
r_scbond_it1.223
r_angle_refined_deg1.184
r_mcangle_it0.833
r_mcbond_it0.496
r_nbtor_refined0.306
r_symmetry_hbond_refined0.204
r_nbd_refined0.203
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.155
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3029
Nucleic Acid Atoms
Solvent Atoms194
Heterogen Atoms120

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction