X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IJApdb entry 2IJA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52912.5 M Ammonium sulfate, 0.1M TRIS, pH 8.5, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.063α = 90
b = 130.063β = 90
c = 111.23γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2006-09-07MSINGLE WAVELENGTH
21x-rayM
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.5418
2

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
1,21.92301000.1337.97.4139603
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)
1,21.921.991000.9976.9

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 2IJA1.923072932265999.8210.2110.20940.2453thin shells21.755
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]
0.0610.061-0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.594
r_dihedral_angle_4_deg13.579
r_dihedral_angle_3_deg12.626
r_dihedral_angle_1_deg6.196
r_scangle_it3.505
r_mcangle_it3.297
r_scbond_it2.59
r_mcbond_it2.458
r_angle_refined_deg1.405
r_angle_other_deg1.039
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.594
r_dihedral_angle_4_deg13.579
r_dihedral_angle_3_deg12.626
r_dihedral_angle_1_deg6.196
r_scangle_it3.505
r_mcangle_it3.297
r_scbond_it2.59
r_mcbond_it2.458
r_angle_refined_deg1.405
r_angle_other_deg1.039
r_mcbond_other0.612
r_symmetry_vdw_other0.293
r_metal_ion_refined0.215
r_nbd_refined0.198
r_nbd_other0.198
r_nbtor_refined0.174
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.146
r_chiral_restr0.087
r_symmetry_vdw_refined0.08
r_nbtor_other0.078
r_bond_refined_d0.017
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4580
Nucleic Acid Atoms
Solvent Atoms278
Heterogen Atoms158

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ARP/wARPmodel building
MolProbitymodel building
Cootmodel building