X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J1D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293Dimethy sulfoxide
Crystal Properties
Matthews coefficientSolvent content
2.2545.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.062α = 90
b = 80.368β = 90
c = 93.712γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102006-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-8BL38B1

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
127097.20.06321.8731896
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)
122.0783.20.3515.95.9

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 REPLACEMENTTHROUGHOUT1J1D25031896168097.040.23170.23020.2588RANDOM46.459
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]
-0.14-2.712.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.538
r_dihedral_angle_4_deg21.113
r_dihedral_angle_3_deg12.823
r_scangle_it4.384
r_dihedral_angle_1_deg4.235
r_scbond_it2.438
r_mcangle_it1.477
r_angle_refined_deg0.971
r_mcbond_it0.732
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.538
r_dihedral_angle_4_deg21.113
r_dihedral_angle_3_deg12.823
r_scangle_it4.384
r_dihedral_angle_1_deg4.235
r_scbond_it2.438
r_mcangle_it1.477
r_angle_refined_deg0.971
r_mcbond_it0.732
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2871
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms27

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction