X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YJ3PDB entry 1YJ3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52980.1 M Bis-Tris, pH 5.5, 1.4 M AMS, 15% glycerol, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.728α = 90
b = 105.728β = 90
c = 50.427γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2009-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM1APS19-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
11.855099.50.1566.211.127549
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)
1.851.8890.50.7148.81258

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 1YJ31.8536.4927534138599.970.1670.1650.2RANDOM14.814
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_deg39.054
r_dihedral_angle_4_deg22.176
r_dihedral_angle_3_deg12.367
r_dihedral_angle_1_deg6.249
r_scangle_it5.344
r_scbond_it3.446
r_mcangle_it1.998
r_angle_refined_deg1.968
r_mcbond_it1.193
r_chiral_restr0.166
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.054
r_dihedral_angle_4_deg22.176
r_dihedral_angle_3_deg12.367
r_dihedral_angle_1_deg6.249
r_scangle_it5.344
r_scbond_it3.446
r_mcangle_it1.998
r_angle_refined_deg1.968
r_mcbond_it1.193
r_chiral_restr0.166
r_bond_refined_d0.028
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2166
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms24

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling