X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YI6PDB ENTRY 1YI6 and 2QO9
experimental modelPDB 2QO9PDB ENTRY 1YI6 and 2QO9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2293.1524% MPD, 0.1M Tris pH 7.2, 10mM Phenol, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
3.160.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.16α = 90
b = 128β = 90
c = 131.35γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.6543.7898.70.068114.110565010552421.6
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)
11.651.7498.50.6082.24.115293

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)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 1YI6 and 2QO91.6540.862105524100253527098.390.156730.155440.18084RANDOM24.827
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]
1.14-0.04-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.038
r_dihedral_angle_4_deg17.048
r_dihedral_angle_3_deg13.741
r_scangle_it9.704
r_scbond_it7.013
r_dihedral_angle_1_deg5.887
r_mcangle_it4.85
r_mcbond_it3.002
r_angle_refined_deg1.557
r_angle_other_deg0.987
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.038
r_dihedral_angle_4_deg17.048
r_dihedral_angle_3_deg13.741
r_scangle_it9.704
r_scbond_it7.013
r_dihedral_angle_1_deg5.887
r_mcangle_it4.85
r_mcbond_it3.002
r_angle_refined_deg1.557
r_angle_other_deg0.987
r_mcbond_other0.854
r_chiral_restr0.098
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4647
Nucleic Acid Atoms
Solvent Atoms582
Heterogen Atoms164

Software

Software
Software NamePurpose
GDAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling