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, 1.1 M AMS, 50 mM NaCl, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6854.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.412α = 90
b = 106.412β = 90
c = 50.422γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2008-11-05MSINGLE 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
11.45099.90.0459.41064180
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)
1.41.421000.2158.33171

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 1YJ31.421.1463914323799.570.1720.1710.19RANDOM11.941
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_deg38.351
r_dihedral_angle_4_deg22.556
r_dihedral_angle_3_deg11.502
r_dihedral_angle_1_deg6.447
r_scangle_it4.655
r_scbond_it3.153
r_angle_refined_deg2.516
r_mcangle_it2.083
r_mcbond_it1.268
r_chiral_restr0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.351
r_dihedral_angle_4_deg22.556
r_dihedral_angle_3_deg11.502
r_dihedral_angle_1_deg6.447
r_scangle_it4.655
r_scbond_it3.153
r_angle_refined_deg2.516
r_mcangle_it2.083
r_mcbond_it1.268
r_chiral_restr0.16
r_bond_refined_d0.031
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2166
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms38

Software

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